├── .github └── workflows │ └── qc.yml ├── .gitignore ├── CONTRIBUTING.md ├── Makefile ├── README.md ├── mappings ├── hp_doid_pistoia.sssom.tsv ├── ma_uberon_pat_impc.sssom.tsv ├── mp_doid_pistoia.sssom.tsv ├── mp_hp_eye_impc.sssom.tsv ├── mp_hp_hwt_impc.sssom.tsv ├── mp_hp_mgi_all.sssom.tsv ├── mp_hp_owt_impc.sssom.tsv ├── mp_hp_pat_impc.sssom.tsv ├── mp_hp_pistoia.sssom.tsv ├── mp_hp_xry_impc.sssom.tsv ├── ordo_doid_pistoia.sssom.tsv ├── ordo_mp_pistoia.sssom.tsv └── pato_hp_pat_impc.sssom.tsv ├── mhmi_analysis.ipynb ├── registry.yml ├── scripts ├── lib.py └── update_registry.py ├── sources ├── README.md ├── impc │ ├── IMPC_EYE_003 MP terms 30 Oct 2020.xlsx │ ├── IMPC_HWT_003 MP terms 30 Oct 2020.xlsx │ ├── IMPC_OWT_003 MP terms 30 Oct 2020.xlsx │ ├── IMPC_PAT_003 MA terms 30 Oct 2020.xlsx │ ├── IMPC_PAT_003 MP terms 30 Oct 2020.xlsx │ ├── IMPC_PAT_003 PATO terms 30 Oct 2020.xlsx │ ├── IMPC_XRY_003 MP terms 30 Oct 2020.xlsx │ ├── README.md │ ├── basic_sssom_metadata.yml │ └── sssom │ │ ├── impc_eye_003_mp_terms_30_oct_2020.tsv │ │ ├── impc_hwt_003_mp_terms_30_oct_2020.tsv │ │ ├── impc_owt_003_mp_terms_30_oct_2020.tsv │ │ ├── impc_pat_003_ma_terms_30_oct_2020.tsv │ │ ├── impc_pat_003_mp_terms_30_oct_2020.tsv │ │ ├── impc_pat_003_pato_terms_30_oct_2020.tsv │ │ └── impc_xry_003_mp_terms_30_oct_2020.tsv ├── mgi │ └── mp-ub-em-ma(2017copy).xlsx ├── mmhcdb │ ├── Apr 2017 MMHCdb, DO, and NCIt tumor terms.xlsx │ └── MMHCdb tumor terms to NCI Thesaurus (Jan 2019 updated June 2020).xlsx ├── pistoia │ ├── calculated_output_hp_doid.csv │ ├── calculated_output_hp_doid.rdf │ ├── calculated_output_mp_doid.csv │ ├── calculated_output_mp_doid.rdf │ ├── calculated_output_mp_hp.csv │ ├── calculated_output_mp_hp.rdf │ ├── calculated_output_ordo_doid.csv │ ├── calculated_output_ordo_doid.rdf │ ├── calculated_output_ordo_hp.csv │ ├── calculated_output_ordo_hp.rdf │ ├── calculated_output_ordo_mp.csv │ └── calculated_output_ordo_mp.rdf └── upheno │ ├── upheno_mapping_lexical.csv │ └── upheno_mapping_logical.csv └── use_cases ├── April2020_KF_Data_Phenotypes_HPO.csv └── README.md /.github/workflows/qc.yml: -------------------------------------------------------------------------------- 1 | # Basic ODK workflow 2 | 3 | name: CI 4 | 5 | # Controls when the action will run. 6 | on: 7 | # Triggers the workflow on push or pull request events but only for the master branch 8 | push: 9 | branches: [ master ] 10 | pull_request: 11 | branches: [ master ] 12 | 13 | # Allows you to run this workflow manually from the Actions tab 14 | workflow_dispatch: 15 | 16 | # A workflow run is made up of one or more jobs that can run sequentially or in parallel 17 | jobs: 18 | sssom_validation: 19 | runs-on: ubuntu-latest 20 | container: obolibrary/odkfull:v1.4.1 21 | steps: 22 | - name: Install latest SSSOM 23 | env: 24 | DEFAULT_BRANCH: master 25 | run: pip install --upgrade pip && pip install -U sssom sssom-schema tsvalid 26 | - uses: actions/checkout@v2 27 | - name: Run Mapping QC checks 28 | env: 29 | DEFAULT_BRANCH: master 30 | run: make validate_mappings 31 | 32 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .idea 2 | .DS_Store 3 | df_kids_first_mapped.csv 4 | .ipynb_checkpoints 5 | ~*.xlsx 6 | tmp/ 7 | .cogs 8 | *.pyc 9 | mappings/*.sssom.ttl 10 | -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- 1 | # Contributing to the Mouse-Human Mapping Commons 2 | 3 | ## Naming conventions: 4 | 5 | 1. Mapping files should be named like: 6 | ``` 7 | subjectsource_objectsource_name_providerid.sssom.tsv 8 | ``` 9 | for example: 10 | ``` 11 | mp_hp_alzheimer_mgi.sssom.tsv 12 | ``` -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- 1 | MAPPINGS_DIR=mappings 2 | 3 | sources/upheno/upheno_mapping_lexical.csv: 4 | wget https://data.monarchinitiative.org/upheno2/current/upheno-release/all/upheno_mapping_lexical.csv -O $@ 5 | 6 | sources/upheno/upheno_mapping_logical.csv: 7 | wget https://data.monarchinitiative.org/upheno2/current/upheno-release/all/upheno_mapping_logical.csv -O $@ 8 | 9 | sources: sources/upheno/upheno_mapping_lexical.csv 10 | sources: sources/upheno/upheno_mapping_logical.csv 11 | 12 | tmp/: 13 | mkdir -p $@ 14 | 15 | 16 | ####################################### 17 | ##### Mapping validation ############# 18 | ####################################### 19 | 20 | validate-%: 21 | tsvalid $(MAPPINGS_DIR)/$*.sssom.tsv --comment "#" 22 | sssom validate $(MAPPINGS_DIR)/$*.sssom.tsv 23 | sssom convert $(MAPPINGS_DIR)/$*.sssom.tsv -o $(MAPPINGS_DIR)/$*.sssom.ttl 24 | 25 | MAPPINGS=$(notdir $(wildcard $(MAPPINGS_DIR)/*.sssom.tsv)) 26 | VALIDATE_MAPPINGS=$(patsubst %.sssom.tsv, validate-%, $(notdir $(wildcard $(MAPPINGS_DIR)/*.sssom.tsv))) 27 | 28 | validate_mappings: $(VALIDATE_MAPPINGS) 29 | 30 | ####################################### 31 | ##### Mappings ####################### 32 | ####################################### 33 | 34 | .PHONY: mappings 35 | mappings: ./scripts/update_registry.py 36 | python $< update-registry -r registry.yml 37 | 38 | ### IMPC Mappings ###### 39 | 40 | mappings/mp_hp_eye_impc.sssom.tsv: sources/impc/sssom/impc_eye_003_mp_terms_30_oct_2020.tsv 41 | sssom parse $< --metadata sources/impc/basic_sssom_metadata.yml -o $@ 42 | sssom annotate $@ --mapping_set_id=mp_hp_eye_impc --mapping_set_description="The IMPC Mouse Morphology Mappings: Eye Morphology Test" -o $@ 43 | 44 | mappings/mp_hp_hwt_impc.sssom.tsv: sources/impc/sssom/impc_hwt_003_mp_terms_30_oct_2020.tsv 45 | sssom parse $< --metadata sources/impc/basic_sssom_metadata.yml -o $@ 46 | sssom annotate $@ --mapping_set_id=mp_hp_hwt_impc --mapping_set_description="The IMPC Mouse Morphology Mappings: Heart Weight Test" -o $@ 47 | 48 | mappings/mp_hp_owt_impc.sssom.tsv: sources/impc/sssom/impc_owt_003_mp_terms_30_oct_2020.tsv 49 | sssom parse $< --metadata sources/impc/basic_sssom_metadata.yml -o $@ 50 | sssom annotate $@ --mapping_set_id=mp_hp_owt_impc --mapping_set_description="The IMPC Mouse Morphology Mappings: Organ Weight Test" -o $@ 51 | 52 | mappings/ma_uberon_pat_impc.sssom.tsv: sources/impc/sssom/impc_pat_003_ma_terms_30_oct_2020.tsv 53 | sssom parse $< --metadata sources/impc/basic_sssom_metadata.yml -o $@ 54 | sssom annotate $@ --mapping_set_id=ma_uberon_pat_impc --mapping_set_description="The IMPC Mouse Morphology Mappings: Gross Pathology & Tissue Collection Test (Anatomy)" -o $@ 55 | 56 | mappings/mp_hp_pat_impc.sssom.tsv: sources/impc/sssom/impc_pat_003_mp_terms_30_oct_2020.tsv 57 | sssom parse $< --metadata sources/impc/basic_sssom_metadata.yml -o $@ 58 | sssom annotate $@ --mapping_set_id=mp_hp_pat_impc --mapping_set_description="The IMPC Mouse Morphology Mappings: Gross Pathology & Tissue Collection Test (Phenotype)" -o $@ 59 | 60 | mappings/pato_hp_pat_impc.sssom.tsv: sources/impc/sssom/impc_pat_003_pato_terms_30_oct_2020.tsv 61 | sssom parse $< --metadata sources/impc/basic_sssom_metadata.yml -o $@ 62 | sssom annotate $@ --mapping_set_id=pato_hp_pat_impc --mapping_set_description="The IMPC Mouse Morphology Mappings: Gross Pathology & Tissue Collection Test (PATO)" -o $@ 63 | 64 | mappings/mp_hp_xry_impc.sssom.tsv: sources/impc/sssom/impc_xry_003_mp_terms_30_oct_2020.tsv 65 | sssom parse $< --metadata sources/impc/basic_sssom_metadata.yml -o $@ 66 | sssom annotate $@ --mapping_set_id=mp_hp_xry_impc --mapping_set_description="The IMPC Mouse Morphology Mappings: X-ray Test" -o $@ 67 | 68 | #### Pistoia mappings #### 69 | 70 | mappings/%_pistoia.sssom.tsv: sources/pistoia/calculated_output_%.rdf 71 | sssom parse $< --input-format alignment-api-xml --prefix-map-mode sssom_default_only -o $@ 72 | sssom annotate $@ --mapping_set_id=$*_pistoia --mapping_provider="https://www.pistoiaalliance.org/projects/current-projects/ontologies-mapping/" --license="https://creativecommons.org/publicdomain/zero/1.0/" --mapping_set_description="The Pistoia Ontology Mappings: $*" -o $@ 73 | 74 | .PHONY: mapping_set_% 75 | mapping_set_%: mappings/%.sssom.tsv 76 | echo "Build $<" -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Mouse-Human Ontology Mapping Initiative (MHMI) 2 | 3 | Studying the phenotypic effects of genes is critical to understanding disease. The phenotypic effects of variants and lesions in large numbers of mouse genes are known due to the accumulated small-scale efforts of the mouse genetics community combined with a large amount of data from genome-wide gene targeting combined with systematic phenotyping. This data can be leveraged to help understand phenotypes not only in mice, but also in humans. A key component required for the integration of human and mouse phenotype data is meaningfully linking the dominant controlled vocabularies (ontologies) used for describing phenotype. For human data the Human Phenotype Ontology is widely used, while for mouse (and rat) data, the Mammalian Phenotype ontology is typically used. 4 | 5 | There are roughly four categories of such mapping approaches: 6 | - __Manually curated mappings:__ An expert determines correspondences between a set of terms from one terminology to another. There are many potential mappings, so most manual curation efforts cater for a specific use case (mappings of phenotypic abnormalities relevant to COVID or Alzheimers, for example). 7 | - __Automated terminological mappings:__ A mapping algorithm takes two or more vocabularies as an input and attempts to create cross-vocabulary links between the terms by using a variety of approaches, from terminological mappings (e.g. based on label, natural language information) to graph-based approaches. These links usally manifest themselves as semantic mapping relations such as exact, broad, narrow and close matches. Mappings of this kind are used for many different use cases, such as knowledge graph integration (https://monarchinitiative.org/) and data aggregation across species. 8 | - __Automated phenotpyic similarity profiles:__ A semantic similarity algorithm takes two or more vocabularies as an input and computes cross-vocabulary links based on semantic similarity measures (e.g. Jaccard, Resnik, Cosine). A semantic similarity profile does not specify a semantic mapping relation such as "exact", "broad" etc (see above). Instead, a pair of terms (for example a mouse and human phenotype term) is associated with a semantic similarity score, usally between 0 and 1, where 1 indicates equivalence. Tools such as [Exomiser](https://www.nature.com/articles/nprot.2015.124), an NHS accredited tool for variant prioritisation and rare disease diagnostics, make heavy use of such phenotypic profiles (especially HP-MP). 9 | - __Computable phenotype definitions:__ Experts define the phenotypes they are using (for example in the Human Phenotype Ontology) using standardised design patterns. Definitions developed this way are interoperable across species and can be exploited by an automated reasoner to compute logical relationships between phenotypes. The most significant efforts in this direction are the [Unified Phenotype Ontology](https://ols.monarchinitiative.org/ontologies/upheno2) and [Phenome.NET](https://pubmed.ncbi.nlm.nih.gov/21737429/), which seek to integrate a large number of different species-specific phenotype ontologies. The leading international effort for developing standardised design patterns is the [Phenotype Reconciliation Effort](https://github.com/obophenotype/upheno/wiki/Phenotype-Ontologies-Reconciliation-Effort). 10 | 11 | The first complication of all these are approaches is that they are _error prone_ for different reasons. The most important reasons are: 12 | 1. _Experts make mistakes_ - both when manually mapping and when defining computable phenotype definitions. Often this is due to ambiguity and variation in the use of language to describe phenotypes. 13 | 2. Some _assumptions_ are made during the mapping process, for example: 14 | - How "rough/vague" a mapping is still acceptable in my case, if an exact match cannot be found (this differs from use case to use case)? Should Fever be mapped to increased body temperature? Should Shivering be mapped to tremors? 15 | - Should I define my phenotype in terms of a physical measurement or observation or in terms of an abnormal biological process (abnormally increased levels of insulin vs abnormally increased insulin production)? 16 | 17 | Furthermore, analysts may expect mappings to different degrees of fuzziness - from crisp 1:1 mappings to n:n mappings determined by phenotypic similarity. 18 | 19 | Next, all approaches are to some degree _incomplete_. Manually curated mappings fill the gap where automated mapping approaches, which largely rely on terminological content, fail to perform well (or at all), but they are usually curated for a specific use case (mappings of phenotypic abnormalities relevant to COVID or Alzheimers, for example). Automatic mappings fail to perform well especially in the area of phenotype due to the often largely divergent terminological content (e.g. preferred labels used by clinical vs. model organism communities). 20 | 21 | Lastly, all approaches have some degree of interdependence. For example, the automated mappings are used to augment cases where no logical definitions / design patterns exist, and logical definitions, in turn, are used to compute mappings. 22 | 23 | The MHMI aims to collect and standardise the dissemination of mouse-phenotype mappings and develop a set of best practices for their use. It leverages advanced tooling to compute mappings and reconcile them with manually curated ones, mitigating the problems above. 24 | 25 | If you are interested in taking part in the Initiative or have use cases that you feel would benefit from these mappings, feel free to join the [Monarch Initiative \& Friends Mailing list](https://groups.google.com/g/monarch-friends) and drop us a message. 26 | 27 | Current active/prospective participants and contributors include: 28 | 29 | | Name | Github | Institution | Role | 30 | | ---- | ------- | ----------- | ----- | 31 | | David Osumi-Sutherland | @dosumis | EMBL-EBI, Monarch Initiative | Coordinator, semantics specialist | 32 | | Susan Bello | @sbello| JAX, MGI, Alliance of Genome Resources | Coordinator, ontology engineer, bio-curator | 33 | | Nicolas Matentzoglu | @matentzn | Semanticly, Monarch Initiative | Coordinator, semantic engineer | 34 | | Anna Anagnostopoulos | @anna-anagnostop| JAX, MGI, Alliance of Genome Resources | ontology engineer, bio-curator | 35 | | Nicole Vasilevsky | @nicolevasilevsky| OHSU, Monarch Initiative | ontology engineer, bio-curator | 36 | | Leigh Carmody | @LCCarmody| JAX, Monarch Initiative | ontology engineer, bio-curator | 37 | | Anna Anagnostopoulos | @anna-anagnostop| JAX, MGI, Alliance of Genome Resources | ontology engineer, bio-curator | 38 | | Thomas Liener | @LLTommy | Pistoia Alliance | semantic engineer | 39 | | Ben Stear | @benstear | Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia | Bioinformatics Scientist I | 40 | | Deanne Taylor | @taylordm | Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia | Director of Bioinformatics | 41 | | Francisco Requena | @frequena | Institut Imagine (Paris) | Ph.D. Student at the Clinical Bioinformatics lab | 42 | | Justin Reese | @justaddcoffee | Lawrence Berkeley Lab | computational biologist | 43 | | Li Xiaoxu | @xianshu-li | Laboratoire de Physiologie Intégrative et Systémique (EPFL) | | 44 | | Violeta Munoz Fuentes | @viomunoz | EMBL-EBI, IMPC | | 45 | | Colin McKerlie | | The Hospital for Sick Children | PI, Comparative Pathologist | 46 | 47 | 48 | ## Specific goals 49 | 50 | ### Collecting all manually curated MP-HP mappings in one place and offering them in a standard format 51 | 52 | - Many manual mappings between MP and HP have been performed for various purposes (COVID (MGI effort), IMPC knockouts, HPO, MPO xrefs, HMDC phenotype headers (MGI Effort)) 53 | - During our uPheno evaluation efforts, we often review automated mapping based on logical inferences. There should be a separate effort to store manually reviewed mappings of automated approaches, which we could use for validation -> when previously validated inferences suddenly disappear, etc. 54 | We will offer these manually curated mappings in a standard format (SSSOM) 55 | 56 | Sub goals: 57 | - Tightly align the upper levels of HP/MP to be able to provide some sanity checking for automated approaches. 58 | 59 | ### Build a conceptual and empirical model for using various forms of automated mappings for stakeholder use cases 60 | 61 | - We will offer a range of automated mappings, from label based, EQ based to semantic similarity and traditional automated mapping approaches using the approaches explored by the OAEI. 62 | - We will document their use cases carefully, and offer simple python notebooks for example evaluations. 63 | - We will develop a model on how to evaluate the effectiveness of automated mapping approaches for the use cases provided by our stakeholders. 64 | - We will determine the set of interventions needed to gradually improve automated approaches in a scalable and sustainable way. 65 | 66 | ### Build infrastructure to combine automated and manually curated mappings 67 | 68 | - There is a huge potential in using automated approaches to validate manual curations. For example, manual mappings could be compared to semantic similarity mappings, with a low semantic similarity indicating problematic choices. 69 | - On the flipside, expert-level mappings can be used as gold standards to evaluate automated mapping approaches. Such information can lead directly to tweaks in the mapping algorithms, but also indicate areas in the ontology that could benefit from more careful axiomatisation or reconciliation. 70 | 71 | ### Initial stakeholder use cases in focus of working group 72 | 73 | - Increasing the clinical relevance of search results on mouse-phenotyping.org (IMPC) of mouse phenotyping in general 74 | - Variant prioritisation 75 | - for diagnosis of children with developmental disorders (CHOP) 76 | - of rare disease patients (Exomiser) 77 | 78 | 79 | ## Stakeholder use cases for mouse-phenotype mappings using ontologies 80 | 81 | *Deanne Taylor*, Director of Bioinformatics, Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia: 82 | 83 | > Congenital birth defects and other developmental disorders likely result from mistiming in the regulated choreography of early development. Perturbations arise from a combination of genetic, epigenetic and environmental factors. There is a great interest (and much work) spent in identifying the specific genetic elements that may contribute to a birth-defect related phenotype Mice are most often used for "genetic laboratories" for comparison to human development. For instance, in gene-to-phenotype studies such as found in the IMPC, a mouse gene is disabled or manipulated, and then the phenotype profile is measured. If the phenotype resembles a human congenital birth defect, we can test for similar changes in genomes from children with that condition. The IMPC classifies phenotypes in Mammalian Phenotype Ontology (MP). Disorders of early development often impact physiology in striking and visible ways, so are easily systematized, and organisms can be classified based on those obsevations. 84 | > Fyler code system was the earliest known example for comprehensively classifying congenital birth defects (https://link.springer.com/chapter/10.1007/978-1-4471-6587-3_12 ). Both the MP and HPO have Fyler code annotations within relevant terms. It would be useful to use the Fyler codes as a “silver standard” (not gold – we’re not there yet!) to determine how well we can match up congenital defect MP and HPO codes. Our simple use case: First, establish a gold standard crosswalk on developmental defects (MP/HPO). Can we identify all truly matching MP/HPO links between Kids First and IMPC, with a crosswalk on at least on Fyler codes or other associated HPO terms 85 | 86 | *Ben Stear*, Bioinformatics Scientist I, Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia: 87 | 88 | > Our main use case is to identify genes of interest from children with cancer/structural birth defects. When a child comes in with a birth defect we want to be able to map their phenotype(s) to the corresponding mouse phenotype(s) in order to take advantage of the extensive gene-knockout research that's been done in mice. Once we have identified the corresponding mouse phenotype, we can then identify genes associated with that phenotype, and then from there get a list of human orthologs for further analysis. 89 | 90 | 91 | *Violeta Munoz-Fuentes*, Mouse Informatics, EMBL-EBI 92 | 93 | > The IMPC is making a catalogue of gene function using the mouse as a model, knocking out one protein gene at a time and recording the phenotype alterations that are observed in the knockout (KO) mice as compared to the wildtype or background strain. By understanding the physiological systems that get affected, the IMPC can link gene with function. Significant phenotype alterations in the KO mice are primarily annotated using the Mammalian Phenotype Ontology, but other ontologies may also be used, as needed (MA, MPATH, PATO, Uberon, EMAPA). 94 | The ultimate goal of the IMPC is to help diagnose human disease. One way to get support for the involvement of a rare variant found in the genome of a patient with a rare disease is by phenorreplication of the patient’s phenotype in an animal model for which that gene has been knocked out (or the variant engineered). In the case of the IMPC, these phenotypes are described primarily using MP terms. Because patients can be / are described using HP terms, there is a need for MP – HP mappings. Some example use cases: 95 | > 1. A clinician has a patient with a rare disease. After sequencing, several genes are identified as potential candidates. The clinician looks up the genes orthologous to the human genes in the IMPC (or other) database. These genes are annotated with significant MP terms, but the clinician needs to see them mapped to HP terms, as the latter are the ones that are used to describe the patient. 96 | > 2. A researcher wants to find genes associated with the cardiovascular function in humans. The researcher looks up “cardiovascular disease” (EFO term) in the GWAS Catalog and 331 variants are reported. Both genes and traits associated with these variants are listed (traits are curated from publications and mapped to the EFO). The researcher wants to see, for the orthologous mouse genes in the IMPC database, which phenotypes are reported in mice, and which ones are not ([issue](https://github.com/obophenotype/mp_hp_mapping/issues/1)). 97 | > 3. A researcher has a subset of IMPC genes that are associated with the cardiovascular function. S/he maps them to the orthologous human genes and looks them up in Open Targets (EFO 3). S/he wants to know which of the phenotype hits reported in humans are also reported in mice and which ones are not. 98 | 99 | 100 | 101 | *Francisco Requena*, Ph.D. Student at the Clinical Bioinformatics lab, Institut Imagine (Paris): 102 | 103 | > My work consists of the interpretation of the mutations found in the DNA of patients with genetic diseases. Phenotypic similarity analysis allows us to take advantage of patients' clinical features to find the causal gene(s). Unfortunately, hundreds of new associations of genetic diseases are discovered every year. Therefore, our current knowledge about the associations of HP terms and genes is limited. As an alternative, we have available extensive information on the effect of altered genes in mouse models with their respective phenotypical consequences. For those genes without HP term annotation, an interesting approach is semantic similarity between MP terms (mouse model) and HP terms (patient). 104 | 105 | 106 | *Li Xiaoxu*, Laboratoire de Physiologie Intégrative et Systémique (EPFL) 107 | 108 | > My project revolves around using our large datasets in mouse genetic reference populations (https://www.systems-genetics.org/, PMID: 29199021) to infer information about humans. One important step in this procedure is matching the many phenotypes we measured in the mice to their human equivalents, hence my interest. 109 | 110 | 111 | -------------------------------------------------------------------------------- /mappings/ma_uberon_pat_impc.sssom.tsv: -------------------------------------------------------------------------------- 1 | # creator_id: orcid:0000-0002-2232-0967 2 | # curie_map: 3 | # MA: http://purl.obolibrary.org/obo/MA_ 4 | # UBERON: http://purl.obolibrary.org/obo/UBERON_ 5 | # owl: http://www.w3.org/2002/07/owl# 6 | # rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# 7 | # rdfs: http://www.w3.org/2000/01/rdf-schema# 8 | # skos: http://www.w3.org/2004/02/skos/core# 9 | # sssom: https://w3id.org/sssom/ 10 | # orcid: https://orcid.org/ 11 | # obo: http://purl.obolibrary.org/obo/ 12 | # semapv: https://w3id.org/semapv/vocab/ 13 | # license: https://creativecommons.org/publicdomain/zero/1.0/ 14 | # mapping_provider: https://www.mousephenotype.org 15 | # mapping_set_description: 'The IMPC Mouse Morphology Mappings: Gross Pathology & Tissue 16 | # Collection Test (Anatomy)' 17 | # mapping_set_id: https://w3id.org/sssom/commons/mouse-human/mappings/ma_uberon_pat_impc.sssom.tsv 18 | subject_id subject_label predicate_id object_id object_label mapping_justification 19 | MA:0000057 brown adipose tissue skos:exactMatch UBERON:0001348 brown adipose tissue semapv:LexicalMatching 20 | MA:0000058 white adipose tissue skos:exactMatch UBERON:0001347 white adipose tissue semapv:LexicalMatching 21 | MA:0000072 heart skos:exactMatch UBERON:0000948 heart semapv:LexicalMatching 22 | MA:0000116 adrenal gland skos:exactMatch UBERON:0002369 adrenal gland semapv:LexicalMatching 23 | MA:0000120 pancreas skos:exactMatch UBERON:0001264 pancreas semapv:LexicalMatching 24 | MA:0000129 thyroid gland skos:exactMatch UBERON:0002046 thyroid gland semapv:LexicalMatching 25 | MA:0000134 bone marrow skos:exactMatch UBERON:0002371 bone marrow semapv:LexicalMatching 26 | MA:0000139 lymph node skos:exactMatch UBERON:0000029 lymph node semapv:LexicalMatching 27 | MA:0000141 spleen skos:exactMatch UBERON:0002106 spleen semapv:LexicalMatching 28 | MA:0000142 thymus skos:exactMatch UBERON:0002370 thymus semapv:LexicalMatching 29 | MA:0000145 mammary gland skos:exactMatch UBERON:0001911 mammary gland semapv:LexicalMatching 30 | MA:0000151 skin skos:closeMatch UBERON:0002199 integument semapv:LogicalReasoning 31 | MA:0000168 brain skos:exactMatch UBERON:0000955 brain semapv:LexicalMatching 32 | MA:0000176 pituitary gland skos:exactMatch UBERON:0000007 pituitary gland semapv:LexicalMatching 33 | MA:0000216 spinal cord skos:exactMatch UBERON:0002240 spinal cord semapv:LexicalMatching 34 | MA:0000236 ear skos:exactMatch UBERON:0001690 ear semapv:LexicalMatching 35 | MA:0000261 eye skos:exactMatch UBERON:0000970 eye semapv:LexicalMatching 36 | MA:0000284 nasal cavity skos:exactMatch UBERON:0001707 nasal cavity semapv:LexicalMatching 37 | MA:0000333 large intestine skos:exactMatch UBERON:0000059 large intestine semapv:LexicalMatching 38 | MA:0000337 small intestine skos:exactMatch UBERON:0002108 small intestine semapv:LexicalMatching 39 | MA:0000346 salivary gland skos:closeMatch UBERON:0001044 saliva-secreting gland semapv:LexicalMatching 40 | MA:0000347 tongue skos:exactMatch UBERON:0001723 tongue semapv:LexicalMatching 41 | MA:0000348 tooth skos:closeMatch UBERON:0001091 calcareous tooth semapv:LexicalMatching 42 | MA:0000352 esophagus skos:exactMatch UBERON:0001043 esophagus semapv:LexicalMatching 43 | MA:0000353 stomach skos:exactMatch UBERON:0000945 stomach semapv:LexicalMatching 44 | MA:0000356 gall bladder skos:exactMatch UBERON:0002110 gall bladder semapv:LexicalMatching 45 | MA:0000358 liver skos:exactMatch UBERON:0002107 liver semapv:LexicalMatching 46 | MA:0000368 kidney skos:exactMatch UBERON:0002113 kidney semapv:LexicalMatching 47 | MA:0000380 urinary bladder skos:exactMatch UBERON:0001255 urinary bladder semapv:LexicalMatching 48 | MA:0000384 ovary skos:exactMatch UBERON:0000992 ovary semapv:LexicalMatching 49 | MA:0000389 uterus skos:exactMatch UBERON:0000995 uterus semapv:LexicalMatching 50 | MA:0000397 epididymis skos:exactMatch UBERON:0001301 epididymis semapv:LexicalMatching 51 | MA:0000404 prostate gland skos:exactMatch UBERON:0002367 prostate gland semapv:LexicalMatching 52 | MA:0000410 seminal vesicle skos:exactMatch UBERON:0000998 seminal vesicle semapv:LexicalMatching 53 | MA:0000411 testis skos:exactMatch UBERON:0000473 testis semapv:LexicalMatching 54 | MA:0000415 lung skos:exactMatch UBERON:0002048 lung semapv:LexicalMatching 55 | MA:0000441 trachea skos:exactMatch UBERON:0003126 trachea semapv:LexicalMatching 56 | MA:0000471 knee joint skos:exactMatch UBERON:0001485 knee joint semapv:LexicalMatching 57 | MA:0000473 subcutaneous adipose tissue skos:exactMatch UBERON:0002190 subcutaneous adipose tissue semapv:LexicalMatching 58 | MA:0001080 trigeminal V ganglion skos:closeMatch UBERON:0001675 trigeminal ganglion semapv:LexicalMatching 59 | MA:0001097 optic II nerve skos:closeMatch UBERON:0000941 cranial nerve II semapv:LogicalReasoning 60 | MA:0001172 sciatic nerve skos:exactMatch UBERON:0001322 sciatic nerve semapv:LexicalMatching 61 | MA:0001331 sternum skos:exactMatch UBERON:0000975 sternum semapv:LexicalMatching 62 | MA:0001359 femur skos:exactMatch UBERON:0000981 femur semapv:LexicalMatching 63 | MA:0001361 tibia skos:exactMatch UBERON:0000979 tibia semapv:LexicalMatching 64 | MA:0001459 bone skos:closeMatch UBERON:0002481 bone tissue semapv:LexicalMatching 65 | MA:0003148 skeletal muscle skos:closeMatch UBERON:0001134 skeletal muscle tissue semapv:LexicalMatching 66 | -------------------------------------------------------------------------------- /mappings/mp_doid_pistoia.sssom.tsv: -------------------------------------------------------------------------------- 1 | # curie_map: 2 | # DOID: http://purl.obolibrary.org/obo/DOID_ 3 | # MP: http://purl.obolibrary.org/obo/MP_ 4 | # owl: http://www.w3.org/2002/07/owl# 5 | # rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# 6 | # rdfs: http://www.w3.org/2000/01/rdf-schema# 7 | # skos: http://www.w3.org/2004/02/skos/core# 8 | # sssom: https://w3id.org/sssom/ 9 | # wikidata: https://www.wikidata.org/wiki/ 10 | # obo: http://purl.obolibrary.org/obo/ 11 | # semapv: https://w3id.org/semapv/vocab/ 12 | # license: https://creativecommons.org/publicdomain/zero/1.0/ 13 | # mapping_provider: https://www.pistoiaalliance.org/projects/current-projects/ontologies-mapping/ 14 | # mapping_set_description: 'The Pistoia Ontology Mappings: mp_doid' 15 | # mapping_set_id: https://w3id.org/sssom/commons/mouse-human/mappings/mp_doid_pistoia.sssom.tsv 16 | # object_source: obo:doid 17 | # subject_source: obo:mp 18 | subject_id predicate_id object_id mapping_justification confidence 19 | MP:0000066 owl:equivalentClass DOID:11476 semapv:UnspecifiedMatching 0.75 20 | MP:0000067 owl:equivalentClass DOID:13533 semapv:UnspecifiedMatching 0.75 21 | MP:0000081 owl:equivalentClass DOID:2340 semapv:UnspecifiedMatching 0.235295 22 | MP:0000111 owl:equivalentClass DOID:674 semapv:UnspecifiedMatching 0.75 23 | MP:0000161 owl:equivalentClass DOID:0060249 semapv:UnspecifiedMatching 0.75 24 | MP:0000189 owl:equivalentClass DOID:9993 semapv:UnspecifiedMatching 0.75 25 | MP:0000231 owl:equivalentClass DOID:10763 semapv:UnspecifiedMatching 0.75 26 | MP:0000284 owl:equivalentClass DOID:6406 semapv:UnspecifiedMatching 0.75 27 | MP:0000315 owl:equivalentClass DOID:582 semapv:UnspecifiedMatching 0.75 28 | MP:0000376 owl:equivalentClass DOID:4409 semapv:UnspecifiedMatching 0.75 29 | MP:0000414 owl:equivalentClass DOID:987 semapv:UnspecifiedMatching 0.75 30 | MP:0000433 owl:equivalentClass DOID:10907 semapv:UnspecifiedMatching 0.75 31 | MP:0000493 owl:equivalentClass DOID:9307 semapv:UnspecifiedMatching 0.75 32 | MP:0000519 owl:equivalentClass DOID:11111 semapv:UnspecifiedMatching 0.75 33 | MP:0000525 owl:equivalentClass DOID:14219 semapv:UnspecifiedMatching 0.75 34 | MP:0000562 owl:equivalentClass DOID:1148 semapv:UnspecifiedMatching 0.75 35 | MP:0000564 owl:equivalentClass DOID:11193 semapv:UnspecifiedMatching 0.75 36 | MP:0000566 owl:equivalentClass DOID:11971 semapv:UnspecifiedMatching 0.75 37 | MP:0000576 owl:equivalentClass DOID:11836 semapv:UnspecifiedMatching 0.75 38 | MP:0000604 owl:equivalentClass DOID:9120 semapv:UnspecifiedMatching 0.75 39 | MP:0000610 owl:equivalentClass DOID:13580 semapv:UnspecifiedMatching 0.75 40 | MP:0000644 owl:equivalentClass DOID:9565 semapv:UnspecifiedMatching 0.75 41 | MP:0000751 owl:equivalentClass DOID:423 semapv:UnspecifiedMatching 0.75 42 | MP:0000917 owl:equivalentClass DOID:14159 semapv:UnspecifiedMatching 0.234695 43 | MP:0001193 owl:equivalentClass DOID:8893 semapv:UnspecifiedMatching 0.75 44 | MP:0001194 owl:equivalentClass DOID:2723 semapv:UnspecifiedMatching 0.75 45 | MP:0001297 owl:equivalentClass DOID:10629 semapv:UnspecifiedMatching 0.75 46 | MP:0001304 owl:equivalentClass DOID:83 semapv:UnspecifiedMatching 0.75 47 | MP:0001326 owl:equivalentClass DOID:8466 semapv:UnspecifiedMatching 0.75 48 | MP:0001344 owl:equivalentClass DOID:0060260 semapv:UnspecifiedMatching 0.75 49 | MP:0001349 owl:equivalentClass DOID:13757 semapv:UnspecifiedMatching 0.75 50 | MP:0001548 owl:equivalentClass DOID:1168 semapv:UnspecifiedMatching 0.23077 51 | MP:0001559 owl:equivalentClass DOID:4195 semapv:UnspecifiedMatching 0.75 52 | MP:0001577 owl:equivalentClass DOID:2355 semapv:UnspecifiedMatching 0.75 53 | MP:0001585 owl:equivalentClass DOID:583 semapv:UnspecifiedMatching 0.75 54 | MP:0001852 owl:equivalentClass DOID:6195 semapv:UnspecifiedMatching 0.75 55 | MP:0001856 owl:equivalentClass DOID:820 semapv:UnspecifiedMatching 0.75 56 | MP:0001857 owl:equivalentClass DOID:1787 semapv:UnspecifiedMatching 0.75 57 | MP:0001864 owl:equivalentClass DOID:865 semapv:UnspecifiedMatching 0.75 58 | MP:0001867 owl:equivalentClass DOID:4483 semapv:UnspecifiedMatching 0.75 59 | MP:0001875 owl:equivalentClass DOID:2518 semapv:UnspecifiedMatching 0.2317075 60 | MP:0001890 owl:equivalentClass DOID:0060668 semapv:UnspecifiedMatching 0.75 61 | MP:0001924 owl:equivalentClass DOID:5223 semapv:UnspecifiedMatching 0.75 62 | MP:0001925 owl:equivalentClass DOID:12336 semapv:UnspecifiedMatching 0.75 63 | MP:0001926 owl:equivalentClass DOID:12336 semapv:UnspecifiedMatching 0.235295 64 | MP:0001948 owl:equivalentClass DOID:9620 semapv:UnspecifiedMatching 0.75 65 | MP:0001953 owl:equivalentClass DOID:11162 semapv:UnspecifiedMatching 0.75 66 | MP:0002001 owl:equivalentClass DOID:1432 semapv:UnspecifiedMatching 0.75 67 | MP:0002006 owl:equivalentClass DOID:14566 semapv:UnspecifiedMatching 0.75 68 | MP:0002269 owl:equivalentClass DOID:767 semapv:UnspecifiedMatching 0.75 69 | MP:0002286 owl:equivalentClass DOID:11383 semapv:UnspecifiedMatching 0.75 70 | MP:0002544 owl:equivalentClass DOID:0050581 semapv:UnspecifiedMatching 0.75 71 | MP:0002654 owl:equivalentClass DOID:649 semapv:UnspecifiedMatching 0.75 72 | MP:0002657 owl:equivalentClass DOID:2256 semapv:UnspecifiedMatching 0.75 73 | MP:0002686 owl:equivalentClass DOID:0111156 semapv:UnspecifiedMatching 0.75 74 | MP:0002708 owl:equivalentClass DOID:585 semapv:UnspecifiedMatching 0.75 75 | MP:0002731 owl:equivalentClass DOID:11372 semapv:UnspecifiedMatching 0.75 76 | MP:0002743 owl:equivalentClass DOID:2921 semapv:UnspecifiedMatching 0.75 77 | MP:0002750 owl:equivalentClass DOID:9370 semapv:UnspecifiedMatching 0.75 78 | MP:0002766 owl:equivalentClass DOID:758 semapv:UnspecifiedMatching 0.75 79 | MP:0002767 owl:equivalentClass DOID:0050545 semapv:UnspecifiedMatching 0.75 80 | MP:0002787 owl:equivalentClass DOID:3765 semapv:UnspecifiedMatching 0.75 81 | MP:0002791 owl:equivalentClass DOID:10602 semapv:UnspecifiedMatching 0.75 82 | MP:0002795 owl:equivalentClass DOID:12930 semapv:UnspecifiedMatching 0.75 83 | MP:0002810 owl:equivalentClass DOID:11252 semapv:UnspecifiedMatching 0.75 84 | MP:0002811 owl:equivalentClass DOID:2361 semapv:UnspecifiedMatching 0.75 85 | MP:0002816 owl:equivalentClass DOID:0060180 semapv:UnspecifiedMatching 0.75 86 | MP:0002872 owl:equivalentClass DOID:8432 semapv:UnspecifiedMatching 0.75 87 | MP:0002926 owl:equivalentClass DOID:10487 semapv:UnspecifiedMatching 0.75 88 | MP:0002927 owl:equivalentClass DOID:1770 semapv:UnspecifiedMatching 0.75 89 | MP:0002984 owl:equivalentClass DOID:0080204 semapv:UnspecifiedMatching 0.2272725 90 | MP:0002993 owl:equivalentClass DOID:848 semapv:UnspecifiedMatching 0.75 91 | MP:0003007 owl:equivalentClass DOID:6307 semapv:UnspecifiedMatching 0.75 92 | MP:0003046 owl:equivalentClass DOID:5082 semapv:UnspecifiedMatching 0.75 93 | MP:0003052 owl:equivalentClass DOID:0060327 semapv:UnspecifiedMatching 0.75 94 | MP:0003054 owl:equivalentClass DOID:0080016 semapv:UnspecifiedMatching 0.75 95 | MP:0003099 owl:equivalentClass DOID:5327 semapv:UnspecifiedMatching 0.75 96 | MP:0003100 owl:equivalentClass DOID:11830 semapv:UnspecifiedMatching 0.75 97 | MP:0003116 owl:equivalentClass DOID:10609 semapv:UnspecifiedMatching 0.75 98 | MP:0003130 owl:equivalentClass DOID:10488 semapv:UnspecifiedMatching 0.75 99 | MP:0003139 owl:equivalentClass DOID:13832 semapv:UnspecifiedMatching 0.75 100 | MP:0003179 owl:equivalentClass DOID:1588 semapv:UnspecifiedMatching 0.75 101 | MP:0003195 owl:equivalentClass DOID:182 semapv:UnspecifiedMatching 0.75 102 | MP:0003197 owl:equivalentClass DOID:12679 semapv:UnspecifiedMatching 0.75 103 | MP:0003254 owl:equivalentClass DOID:9446 semapv:UnspecifiedMatching 0.25 104 | MP:0003258 owl:equivalentClass DOID:12642 semapv:UnspecifiedMatching 0.75 105 | MP:0003267 owl:equivalentClass DOID:2089 semapv:UnspecifiedMatching 0.75 106 | MP:0003270 owl:equivalentClass DOID:8437 semapv:UnspecifiedMatching 0.75 107 | MP:0003273 owl:equivalentClass DOID:1724 semapv:UnspecifiedMatching 0.75 108 | MP:0003276 owl:equivalentClass DOID:10485 semapv:UnspecifiedMatching 0.75 109 | MP:0003282 owl:equivalentClass DOID:10808 semapv:UnspecifiedMatching 0.75 110 | MP:0003286 owl:equivalentClass DOID:8534 semapv:UnspecifiedMatching 0.75 111 | MP:0003294 owl:equivalentClass DOID:8446 semapv:UnspecifiedMatching 0.75 112 | MP:0003305 owl:equivalentClass DOID:3127 semapv:UnspecifiedMatching 0.75 113 | MP:0003307 owl:equivalentClass DOID:12639 semapv:UnspecifiedMatching 0.75 114 | MP:0003319 owl:equivalentClass DOID:0060328 semapv:UnspecifiedMatching 0.75 115 | MP:0003328 owl:equivalentClass DOID:10762 semapv:UnspecifiedMatching 0.75 116 | MP:0003335 owl:equivalentClass DOID:13316 semapv:UnspecifiedMatching 0.75 117 | MP:0003347 owl:equivalentClass DOID:2444 semapv:UnspecifiedMatching 0.75 118 | MP:0003348 owl:equivalentClass DOID:9406 semapv:UnspecifiedMatching 0.75 119 | MP:0003376 owl:equivalentClass DOID:13938 semapv:UnspecifiedMatching 0.75 120 | MP:0003390 owl:equivalentClass DOID:4977 semapv:UnspecifiedMatching 0.75 121 | MP:0003415 owl:equivalentClass DOID:9286 semapv:UnspecifiedMatching 0.75 122 | MP:0003446 owl:equivalentClass DOID:0080204 semapv:UnspecifiedMatching 0.75 123 | MP:0003506 owl:equivalentClass DOID:2449 semapv:UnspecifiedMatching 0.75 124 | MP:0003548 owl:equivalentClass DOID:6432 semapv:UnspecifiedMatching 0.75 125 | MP:0003554 owl:equivalentClass DOID:2712 semapv:UnspecifiedMatching 0.75 126 | MP:0003560 owl:equivalentClass DOID:8398 semapv:UnspecifiedMatching 0.75 127 | MP:0003561 owl:equivalentClass DOID:7148 semapv:UnspecifiedMatching 0.75 128 | MP:0003565 owl:equivalentClass DOID:14427 semapv:UnspecifiedMatching 0.2368425 129 | MP:0003587 owl:equivalentClass DOID:5199 semapv:UnspecifiedMatching 0.2368425 130 | MP:0003592 owl:equivalentClass DOID:1829 semapv:UnspecifiedMatching 0.2428575 131 | MP:0003606 owl:equivalentClass DOID:1074 semapv:UnspecifiedMatching 0.75 132 | MP:0003623 owl:equivalentClass DOID:9912 semapv:UnspecifiedMatching 0.75 133 | MP:0003624 owl:equivalentClass DOID:2983 semapv:UnspecifiedMatching 0.75 134 | MP:0003665 owl:equivalentClass DOID:4692 semapv:UnspecifiedMatching 0.75 135 | MP:0003689 owl:equivalentClass DOID:539 semapv:UnspecifiedMatching 0.75 136 | MP:0003746 owl:equivalentClass DOID:9637 semapv:UnspecifiedMatching 0.75 137 | MP:0003828 owl:equivalentClass DOID:11396 semapv:UnspecifiedMatching 0.75 138 | MP:0003865 owl:equivalentClass DOID:1602 semapv:UnspecifiedMatching 0.234695 139 | MP:0003924 owl:equivalentClass DOID:3827 semapv:UnspecifiedMatching 0.75 140 | MP:0003985 owl:equivalentClass DOID:0050855 semapv:UnspecifiedMatching 0.75 141 | MP:0003991 owl:equivalentClass DOID:2349 semapv:UnspecifiedMatching 0.75 142 | MP:0004020 owl:equivalentClass DOID:8488 semapv:UnspecifiedMatching 0.75 143 | MP:0004119 owl:equivalentClass DOID:4500 semapv:UnspecifiedMatching 0.75 144 | MP:0004133 owl:equivalentClass DOID:0050545 semapv:UnspecifiedMatching 0.75 145 | MP:0004254 owl:equivalentClass DOID:9246 semapv:UnspecifiedMatching 0.75 146 | MP:0004270 owl:equivalentClass DOID:0060145 semapv:UnspecifiedMatching 0.75 147 | MP:0004510 owl:equivalentClass DOID:633 semapv:UnspecifiedMatching 0.75 148 | MP:0004547 owl:equivalentClass DOID:6050 semapv:UnspecifiedMatching 0.75 149 | MP:0004684 owl:equivalentClass DOID:90 semapv:UnspecifiedMatching 0.2421875 150 | MP:0004740 owl:equivalentClass DOID:10003 semapv:UnspecifiedMatching 0.75 151 | MP:0004749 owl:equivalentClass DOID:0050563 semapv:UnspecifiedMatching 0.75 152 | MP:0004750 owl:equivalentClass DOID:0050563 semapv:UnspecifiedMatching 0.2340425 153 | MP:0004897 owl:equivalentClass DOID:12185 semapv:UnspecifiedMatching 0.75 154 | MP:0004947 owl:equivalentClass DOID:2723 semapv:UnspecifiedMatching 0.75 155 | MP:0005036 owl:equivalentClass DOID:13250 semapv:UnspecifiedMatching 0.75 156 | MP:0005152 owl:equivalentClass DOID:12450 semapv:UnspecifiedMatching 0.75 157 | MP:0005157 owl:equivalentClass DOID:4621 semapv:UnspecifiedMatching 0.75 158 | MP:0005159 owl:equivalentClass DOID:14227 semapv:UnspecifiedMatching 0.75 159 | MP:0005190 owl:equivalentClass DOID:1019 semapv:UnspecifiedMatching 0.75 160 | MP:0005244 owl:equivalentClass DOID:11482 semapv:UnspecifiedMatching 0.75 161 | MP:0005245 owl:equivalentClass DOID:801 semapv:UnspecifiedMatching 0.75 162 | MP:0005251 owl:equivalentClass DOID:9423 semapv:UnspecifiedMatching 0.75 163 | MP:0005254 owl:equivalentClass DOID:540 semapv:UnspecifiedMatching 0.75 164 | MP:0005255 owl:equivalentClass DOID:1143 semapv:UnspecifiedMatching 0.75 165 | MP:0005256 owl:equivalentClass DOID:9840 semapv:UnspecifiedMatching 0.75 166 | MP:0005258 owl:equivalentClass DOID:9282 semapv:UnspecifiedMatching 0.75 167 | MP:0005260 owl:equivalentClass DOID:790 semapv:UnspecifiedMatching 0.75 168 | MP:0005261 owl:equivalentClass DOID:12271 semapv:UnspecifiedMatching 0.75 169 | MP:0005262 owl:equivalentClass DOID:12270 semapv:UnspecifiedMatching 0.75 170 | MP:0005264 owl:equivalentClass DOID:0050851 semapv:UnspecifiedMatching 0.75 171 | MP:0005279 owl:equivalentClass DOID:8986 semapv:UnspecifiedMatching 0.75 172 | MP:0005297 owl:equivalentClass DOID:0080073 semapv:UnspecifiedMatching 0.75 173 | MP:0005302 owl:equivalentClass DOID:12143 semapv:UnspecifiedMatching 0.75 174 | MP:0005312 owl:equivalentClass DOID:118 semapv:UnspecifiedMatching 0.75 175 | MP:0005323 owl:equivalentClass DOID:543 semapv:UnspecifiedMatching 0.75 176 | MP:0005330 owl:equivalentClass DOID:0050700 semapv:UnspecifiedMatching 0.75 177 | MP:0005414 owl:equivalentClass DOID:13619 semapv:UnspecifiedMatching 0.75 178 | MP:0005415 owl:equivalentClass DOID:1852 semapv:UnspecifiedMatching 0.75 179 | MP:0005421 owl:equivalentClass DOID:3144 semapv:UnspecifiedMatching 0.75 180 | MP:0005422 owl:equivalentClass DOID:4254 semapv:UnspecifiedMatching 0.75 181 | MP:0005505 owl:equivalentClass DOID:2228 semapv:UnspecifiedMatching 0.75 182 | MP:0005515 owl:equivalentClass DOID:13141 semapv:UnspecifiedMatching 0.75 183 | MP:0005544 owl:equivalentClass DOID:11547 semapv:UnspecifiedMatching 0.241935 184 | MP:0005604 owl:equivalentClass DOID:0060695 semapv:UnspecifiedMatching 0.75 185 | MP:0005638 owl:equivalentClass DOID:2352 semapv:UnspecifiedMatching 0.75 186 | MP:0005639 owl:equivalentClass DOID:12119 semapv:UnspecifiedMatching 0.75 187 | MP:0005654 owl:equivalentClass DOID:13268 semapv:UnspecifiedMatching 0.75 188 | MP:0006034 owl:equivalentClass DOID:0080108 semapv:UnspecifiedMatching 0.75 189 | MP:0006050 owl:equivalentClass DOID:3770 semapv:UnspecifiedMatching 0.75 190 | MP:0006061 owl:equivalentClass DOID:0060856 semapv:UnspecifiedMatching 0.75 191 | MP:0006077 owl:equivalentClass DOID:0060320 semapv:UnspecifiedMatching 0.75 192 | MP:0006093 owl:equivalentClass DOID:11294 semapv:UnspecifiedMatching 0.75 193 | MP:0006117 owl:equivalentClass DOID:1712 semapv:UnspecifiedMatching 0.75 194 | MP:0006118 owl:equivalentClass DOID:5232 semapv:UnspecifiedMatching 0.75 195 | MP:0006120 owl:equivalentClass DOID:988 semapv:UnspecifiedMatching 0.75 196 | MP:0006122 owl:equivalentClass DOID:1754 semapv:UnspecifiedMatching 0.75 197 | MP:0006124 owl:equivalentClass DOID:4078 semapv:UnspecifiedMatching 0.75 198 | MP:0006125 owl:equivalentClass DOID:5644 semapv:UnspecifiedMatching 0.75 199 | MP:0006128 owl:equivalentClass DOID:6420 semapv:UnspecifiedMatching 0.75 200 | MP:0006136 owl:equivalentClass DOID:799 semapv:UnspecifiedMatching 0.75 201 | MP:0006138 owl:equivalentClass DOID:6000 semapv:UnspecifiedMatching 0.75 202 | MP:0006151 owl:equivalentClass DOID:11782 semapv:UnspecifiedMatching 0.75 203 | MP:0006153 owl:equivalentClass DOID:9834 semapv:UnspecifiedMatching 0.75 204 | MP:0006159 owl:equivalentClass DOID:0050633 semapv:UnspecifiedMatching 0.75 205 | MP:0006164 owl:equivalentClass DOID:1570 semapv:UnspecifiedMatching 0.75 206 | MP:0006165 owl:equivalentClass DOID:12397 semapv:UnspecifiedMatching 0.75 207 | MP:0006177 owl:equivalentClass DOID:980 semapv:UnspecifiedMatching 0.23611 208 | MP:0006186 owl:equivalentClass DOID:0050855 semapv:UnspecifiedMatching 0.2333325 209 | MP:0006190 owl:equivalentClass DOID:12510 semapv:UnspecifiedMatching 0.75 210 | MP:0006191 owl:equivalentClass DOID:11653 semapv:UnspecifiedMatching 0.2439025 211 | MP:0006194 owl:equivalentClass DOID:9368 semapv:UnspecifiedMatching 0.75 212 | MP:0006198 owl:equivalentClass DOID:11175 semapv:UnspecifiedMatching 0.75 213 | MP:0006199 owl:equivalentClass DOID:9837 semapv:UnspecifiedMatching 0.75 214 | MP:0006222 owl:equivalentClass DOID:1891 semapv:UnspecifiedMatching 0.75 215 | MP:0006248 owl:equivalentClass DOID:12959 semapv:UnspecifiedMatching 0.75 216 | MP:0006261 owl:equivalentClass DOID:0060850 semapv:UnspecifiedMatching 0.75 217 | MP:0006278 owl:equivalentClass DOID:3627 semapv:UnspecifiedMatching 0.75 218 | MP:0008387 owl:equivalentClass DOID:11759 semapv:UnspecifiedMatching 0.75 219 | MP:0008388 owl:equivalentClass DOID:0050642 semapv:UnspecifiedMatching 0.75 220 | MP:0008389 owl:equivalentClass DOID:0050642 semapv:UnspecifiedMatching 0.24138 221 | MP:0008541 owl:equivalentClass DOID:12986 semapv:UnspecifiedMatching 0.75 222 | MP:0008543 owl:equivalentClass DOID:0060224 semapv:UnspecifiedMatching 0.75 223 | MP:0008869 owl:equivalentClass DOID:3781 semapv:UnspecifiedMatching 0.75 224 | MP:0008970 owl:equivalentClass DOID:9574 semapv:UnspecifiedMatching 0.75 225 | MP:0009274 owl:equivalentClass DOID:11211 semapv:UnspecifiedMatching 0.75 226 | MP:0009445 owl:equivalentClass DOID:10573 semapv:UnspecifiedMatching 0.75 227 | MP:0009578 owl:equivalentClass DOID:0060341 semapv:UnspecifiedMatching 0.75 228 | MP:0009644 owl:equivalentClass DOID:4676 semapv:UnspecifiedMatching 0.75 229 | MP:0009668 owl:equivalentClass DOID:0060329 semapv:UnspecifiedMatching 0.75 230 | MP:0009699 owl:equivalentClass DOID:14118 semapv:UnspecifiedMatching 0.75 231 | MP:0009744 owl:equivalentClass DOID:1148 semapv:UnspecifiedMatching 0.75 232 | MP:0009792 owl:equivalentClass DOID:8741 semapv:UnspecifiedMatching 0.75 233 | MP:0009825 owl:equivalentClass DOID:8463 semapv:UnspecifiedMatching 0.24 234 | MP:0009860 owl:equivalentClass DOID:11664 semapv:UnspecifiedMatching 0.75 235 | MP:0009877 owl:equivalentClass DOID:203 semapv:UnspecifiedMatching 0.75 236 | MP:0010033 owl:equivalentClass DOID:5334 semapv:UnspecifiedMatching 0.75 237 | MP:0010139 owl:equivalentClass DOID:519 semapv:UnspecifiedMatching 0.75 238 | MP:0010140 owl:equivalentClass DOID:864 semapv:UnspecifiedMatching 0.75 239 | MP:0010141 owl:equivalentClass DOID:9317 semapv:UnspecifiedMatching 0.75 240 | MP:0010146 owl:equivalentClass DOID:0060321 semapv:UnspecifiedMatching 0.75 241 | MP:0010260 owl:equivalentClass DOID:0050537 semapv:UnspecifiedMatching 0.2448975 242 | MP:0010402 owl:equivalentClass DOID:1657 semapv:UnspecifiedMatching 0.75 243 | MP:0010403 owl:equivalentClass DOID:1882 semapv:UnspecifiedMatching 0.75 244 | MP:0010405 owl:equivalentClass DOID:13620 semapv:UnspecifiedMatching 0.233765 245 | MP:0010412 owl:equivalentClass DOID:0050651 semapv:UnspecifiedMatching 0.75 246 | MP:0010452 owl:equivalentClass DOID:11295 semapv:UnspecifiedMatching 0.2439025 247 | MP:0010471 owl:equivalentClass DOID:1929 semapv:UnspecifiedMatching 0.2410725 248 | MP:0010478 owl:equivalentClass DOID:10941 semapv:UnspecifiedMatching 0.75 249 | MP:0010479 owl:equivalentClass DOID:10941 semapv:UnspecifiedMatching 0.75 250 | MP:0010519 owl:equivalentClass DOID:0050820 semapv:UnspecifiedMatching 0.75 251 | MP:0010530 owl:equivalentClass DOID:0060688 semapv:UnspecifiedMatching 0.75 252 | MP:0010658 owl:equivalentClass DOID:14004 semapv:UnspecifiedMatching 0.2340425 253 | MP:0010659 owl:equivalentClass DOID:7693 semapv:UnspecifiedMatching 0.234695 254 | MP:0010711 owl:equivalentClass DOID:0060282 semapv:UnspecifiedMatching 0.75 255 | MP:0010716 owl:equivalentClass DOID:11975 semapv:UnspecifiedMatching 0.2317075 256 | MP:0010717 owl:equivalentClass DOID:11975 semapv:UnspecifiedMatching 0.2325575 257 | MP:0010822 owl:equivalentClass DOID:1673 semapv:UnspecifiedMatching 0.75 258 | MP:0010883 owl:equivalentClass DOID:3227 semapv:UnspecifiedMatching 0.242425 259 | MP:0010922 owl:equivalentClass DOID:841 semapv:UnspecifiedMatching 0.75 260 | MP:0010998 owl:equivalentClass DOID:12120 semapv:UnspecifiedMatching 0.75 261 | MP:0011012 owl:equivalentClass DOID:9563 semapv:UnspecifiedMatching 0.75 262 | MP:0011164 owl:equivalentClass DOID:1526 semapv:UnspecifiedMatching 0.75 263 | MP:0011174 owl:equivalentClass DOID:811 semapv:UnspecifiedMatching 0.75 264 | MP:0011403 owl:equivalentClass DOID:11400 semapv:UnspecifiedMatching 0.75 265 | MP:0011404 owl:equivalentClass DOID:2744 semapv:UnspecifiedMatching 0.75 266 | MP:0011420 owl:equivalentClass DOID:1439 semapv:UnspecifiedMatching 0.75 267 | MP:0011491 owl:equivalentClass DOID:0111145 semapv:UnspecifiedMatching 0.75 268 | MP:0011515 owl:equivalentClass DOID:3326 semapv:UnspecifiedMatching 0.75 269 | MP:0011516 owl:equivalentClass DOID:0050461 semapv:UnspecifiedMatching 0.75 270 | MP:0011570 owl:equivalentClass DOID:9164 semapv:UnspecifiedMatching 0.75 271 | MP:0011665 owl:equivalentClass DOID:0060770 semapv:UnspecifiedMatching 0.23077 272 | MP:0011747 owl:equivalentClass DOID:4971 semapv:UnspecifiedMatching 0.75 273 | MP:0011758 owl:equivalentClass DOID:12510 semapv:UnspecifiedMatching 0.2333325 274 | MP:0011763 owl:equivalentClass DOID:1343 semapv:UnspecifiedMatching 0.75 275 | MP:0011767 owl:equivalentClass DOID:4022 semapv:UnspecifiedMatching 0.75 276 | MP:0011801 owl:equivalentClass DOID:12577 semapv:UnspecifiedMatching 0.24359 277 | MP:0011802 owl:equivalentClass DOID:9365 semapv:UnspecifiedMatching 0.75 278 | MP:0012121 owl:equivalentClass DOID:0060252 semapv:UnspecifiedMatching 0.75 279 | MP:0012171 owl:equivalentClass DOID:12215 semapv:UnspecifiedMatching 0.75 280 | MP:0012259 owl:equivalentClass DOID:1088 semapv:UnspecifiedMatching 0.75 281 | MP:0012491 owl:equivalentClass DOID:11527 semapv:UnspecifiedMatching 0.2272725 282 | MP:0012545 owl:equivalentClass DOID:327 semapv:UnspecifiedMatching 0.75 283 | MP:0012551 owl:equivalentClass DOID:0050758 semapv:UnspecifiedMatching 0.75 284 | MP:0012552 owl:equivalentClass DOID:3650 semapv:UnspecifiedMatching 0.75 285 | MP:0013148 owl:equivalentClass DOID:10690 semapv:UnspecifiedMatching 0.75 286 | MP:0013251 owl:equivalentClass DOID:11623 semapv:UnspecifiedMatching 0.75 287 | MP:0013335 owl:equivalentClass DOID:914 semapv:UnspecifiedMatching 0.75 288 | MP:0013370 owl:equivalentClass DOID:11156 semapv:UnspecifiedMatching 0.75 289 | MP:0013371 owl:equivalentClass DOID:11155 semapv:UnspecifiedMatching 0.75 290 | MP:0013451 owl:equivalentClass DOID:13929 semapv:UnspecifiedMatching 0.2314825 291 | MP:0013466 owl:equivalentClass DOID:12895 semapv:UnspecifiedMatching 0.75 292 | MP:0013479 owl:equivalentClass DOID:13452 semapv:UnspecifiedMatching 0.75 293 | MP:0013546 owl:equivalentClass DOID:0110214 semapv:UnspecifiedMatching 0.75 294 | MP:0013731 owl:equivalentClass DOID:10997 semapv:UnspecifiedMatching 0.75 295 | MP:0013732 owl:equivalentClass DOID:13717 semapv:UnspecifiedMatching 0.75 296 | MP:0013753 owl:equivalentClass DOID:0060313 semapv:UnspecifiedMatching 0.75 297 | MP:0013806 owl:equivalentClass DOID:936 semapv:UnspecifiedMatching 0.75 298 | MP:0014086 owl:equivalentClass DOID:255 semapv:UnspecifiedMatching 0.75 299 | MP:0014187 owl:equivalentClass DOID:11997 semapv:UnspecifiedMatching 0.75 300 | MP:0020038 owl:equivalentClass DOID:4448 semapv:UnspecifiedMatching 0.2327575 301 | MP:0020050 owl:equivalentClass DOID:0090122 semapv:UnspecifiedMatching 0.2314825 302 | MP:0020225 owl:equivalentClass DOID:10159 semapv:UnspecifiedMatching 0.75 303 | MP:0020400 owl:equivalentClass DOID:9266 semapv:UnspecifiedMatching 0.75 304 | MP:0020461 owl:equivalentClass DOID:0080193 semapv:UnspecifiedMatching 0.75 305 | MP:0030141 owl:equivalentClass DOID:13934 semapv:UnspecifiedMatching 0.75 306 | MP:0030222 owl:equivalentClass DOID:205 semapv:UnspecifiedMatching 0.75 307 | MP:0030226 owl:equivalentClass DOID:7439 semapv:UnspecifiedMatching 0.2285725 308 | MP:0030449 owl:equivalentClass DOID:12661 semapv:UnspecifiedMatching 0.75 309 | -------------------------------------------------------------------------------- /mappings/mp_hp_eye_impc.sssom.tsv: -------------------------------------------------------------------------------- 1 | # creator_id: orcid:0000-0002-2232-0967 2 | # curie_map: 3 | # HP: http://purl.obolibrary.org/obo/HP_ 4 | # MP: http://purl.obolibrary.org/obo/MP_ 5 | # owl: http://www.w3.org/2002/07/owl# 6 | # rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# 7 | # rdfs: http://www.w3.org/2000/01/rdf-schema# 8 | # skos: http://www.w3.org/2004/02/skos/core# 9 | # sssom: https://w3id.org/sssom/ 10 | # orcid: https://orcid.org/ 11 | # obo: http://purl.obolibrary.org/obo/ 12 | # semapv: https://w3id.org/semapv/vocab/ 13 | # license: https://creativecommons.org/publicdomain/zero/1.0/ 14 | # mapping_provider: https://www.mousephenotype.org 15 | # mapping_set_description: 'The IMPC Mouse Morphology Mappings: Eye Morphology Test' 16 | # mapping_set_id: https://w3id.org/sssom/commons/mouse-human/mappings/mp_hp_eye_impc.sssom.tsv 17 | subject_id subject_label predicate_id object_id object_label mapping_justification 18 | MP:0001289 persistence of hyaloid vascular system skos:closeMatch HP:0007968 Remnants of the hyaloid vascular system semapv:LexicalMatching 19 | MP:0001293 anophthalmia skos:exactMatch HP:0000528 Anophthalmia semapv:LexicalMatching 20 | MP:0001303 abnormal lens morphology skos:closeMatch HP:0000517 Abnormality of the lens semapv:LexicalMatching 21 | MP:0001304 cataract skos:exactMatch HP:0000518 Cataract semapv:LexicalMatching 22 | MP:0001307 fused cornea and lens skos:closeMatch HP:0011485 Corneolenticular adhesion semapv:LogicalReasoning 23 | MP:0001312 abnormal cornea morphology skos:exactMatch HP:0000481 Abnormal cornea morphology semapv:LexicalMatching 24 | MP:0001314 corneal opacity skos:exactMatch HP:0007957 Corneal opacity semapv:LexicalMatching 25 | MP:0001319 irregularly shaped pupil skos:exactMatch HP:0025309 Abnormal pupil shape semapv:LogicalReasoning 26 | MP:0001325 abnormal retina morphology skos:closeMatch HP:0000479 Abnormal retinal morphology semapv:LexicalMatching 27 | MP:0001340 abnormal eyelid morphology skos:exactMatch HP:0000492 Abnormal eyelid morphology semapv:LexicalMatching 28 | MP:0001349 excessive tearing skos:closeMatch HP:0009926 Epiphora semapv:LogicalReasoning 29 | MP:0002546 mydriasis skos:exactMatch HP:0011499 Mydriasis semapv:LexicalMatching 30 | MP:0002638 abnormal pupillary reflex skos:closeMatch HP:0007695 Abnormal pupillary light reflex semapv:LexicalMatching 31 | MP:0002699 abnormal vitreous body morphology skos:closeMatch HP:0004327 Abnormal vitreous humor morphology semapv:LogicalReasoning 32 | MP:0002750 exophthalmos skos:closeMatch HP:0000520 Proptosis semapv:LogicalReasoning 33 | MP:0002792 abnormal retinal vasculature morphology skos:closeMatch HP:0008046 Abnormal retinal vascular morphology semapv:LexicalMatching 34 | MP:0003731 abnormal retinal outer nuclear layer morphology skos:closeMatch HP:0000479 Abnormal retinal morphology semapv:LogicalReasoning 35 | MP:0003731 abnormal retinal outer nuclear layer morphology skos:closeMatch HP:0000479 Abnormal retinal morphology semapv:LogicalReasoning 36 | MP:0003733 abnormal retinal inner nuclear layer morphology skos:closeMatch HP:0000479 Abnormal retinal morphology semapv:LogicalReasoning 37 | MP:0003733 abnormal retinal inner nuclear layer morphology skos:closeMatch HP:0000479 Abnormal retinal morphology semapv:LogicalReasoning 38 | MP:0004222 iris synechia skos:closeMatch HP:0011483 Anterior synechiae of the anterior chamber semapv:LexicalMatching 39 | MP:0004222 iris synechia skos:closeMatch HP:0011484 Posterior synechiae of the anterior chamber semapv:LexicalMatching 40 | MP:0005102 abnormal iris pigmentation skos:exactMatch HP:0008034 Abnormal iris pigmentation semapv:LexicalMatching 41 | MP:0005176 eyelids fail to open skos:closeMatch HP:0009755 Ankyloblepharon semapv:LogicalReasoning 42 | MP:0005287 narrow eye opening skos:closeMatch HP:0045025 Narrow palpebral fissure semapv:LogicalReasoning 43 | MP:0005542 corneal vascularization skos:closeMatch HP:0011496 Corneal neovascularization semapv:LexicalMatching 44 | MP:0005543 decreased cornea thickness skos:exactMatch HP:0100689 Decreased corneal thickness semapv:LexicalMatching 45 | MP:0005544 corneal deposits skos:closeMatch HP:0000531 Corneal crystals semapv:LogicalReasoning 46 | MP:0006203 eye hemorrhage skos:exactMatch HP:0011885 Hemorrhage of the eye semapv:LexicalMatching 47 | MP:0006241 abnormal placement of pupils skos:closeMatch HP:0009918 Ectopia pupillae semapv:LogicalReasoning 48 | MP:0006241 constricted or contracted pupil skos:closeMatch HP:0025309 Abnormal pupil shape semapv:LogicalReasoning 49 | MP:0008259 abnormal optic disc morphology skos:closeMatch HP:0012795 Abnormality of the optic disc semapv:LexicalMatching 50 | MP:0009825 cornea ulcer skos:closeMatch HP:0012804 Corneal ulceration semapv:LexicalMatching 51 | MP:0010097 abnormal retinal blood vessel morphology skos:closeMatch HP:0008046 Abnormal retinal vascular morphology semapv:LexicalMatching 52 | MP:0010097 abnormal retinal blood vessel morphology skos:closeMatch HP:0008046 Abnormal retinal vascular morphology semapv:LexicalMatching 53 | MP:0011959 abnormal eye posterior chamber depth skos:closeMatch HP:0004329 Abnormal posterior eye segment morphology semapv:LogicalReasoning 54 | MP:0011959 abnormal eye posterior chamber depth skos:closeMatch HP:0004329 Abnormal posterior eye segment morphology semapv:LogicalReasoning 55 | MP:0011960 abnormal eye anterior chamber depth skos:closeMatch HP:0000593 Abnormal anterior chamber morphology semapv:LogicalReasoning 56 | MP:0011960 abnormal eye anterior chamber depth skos:closeMatch HP:0000593 Abnormal anterior chamber morphology semapv:LogicalReasoning 57 | MP:0011962 increased cornea thickness skos:exactMatch HP:0011487 Increased corneal thickness semapv:LexicalMatching 58 | MP:0011962 increased cornea thickness skos:exactMatch HP:0011487 Increased corneal thickness semapv:LexicalMatching 59 | MP:0011964 increased total retina thickness skos:closeMatch HP:0000479 Abnormal retinal morphology semapv:LogicalReasoning 60 | MP:0011964 increased total retina thickness skos:closeMatch HP:0000479 Abnormal retinal morphology semapv:LogicalReasoning 61 | MP:0011965 decreased total retina thickness skos:closeMatch HP:0030329 Retinal thinning semapv:LogicalReasoning 62 | MP:0011965 decreased total retina thickness skos:closeMatch HP:0030329 Retinal thinning semapv:LogicalReasoning 63 | MP:0012121 sclerocornea skos:exactMatch HP:0000647 Sclerocornea semapv:LexicalMatching 64 | MP:0012122 abnormal iris transillumination skos:closeMatch HP:0012805 Iris transillumination defect semapv:LogicalReasoning 65 | -------------------------------------------------------------------------------- /mappings/mp_hp_hwt_impc.sssom.tsv: -------------------------------------------------------------------------------- 1 | # creator_id: orcid:0000-0002-2232-0967 2 | # curie_map: 3 | # HP: http://purl.obolibrary.org/obo/HP_ 4 | # MP: http://purl.obolibrary.org/obo/MP_ 5 | # owl: http://www.w3.org/2002/07/owl# 6 | # rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# 7 | # rdfs: http://www.w3.org/2000/01/rdf-schema# 8 | # skos: http://www.w3.org/2004/02/skos/core# 9 | # sssom: https://w3id.org/sssom/ 10 | # orcid: https://orcid.org/ 11 | # obo: http://purl.obolibrary.org/obo/ 12 | # semapv: https://w3id.org/semapv/vocab/ 13 | # license: https://creativecommons.org/publicdomain/zero/1.0/ 14 | # mapping_provider: https://www.mousephenotype.org 15 | # mapping_set_description: 'The IMPC Mouse Morphology Mappings: Heart Weight Test' 16 | # mapping_set_id: https://w3id.org/sssom/commons/mouse-human/mappings/mp_hp_hwt_impc.sssom.tsv 17 | subject_id subject_label predicate_id object_id object_label mapping_justification 18 | MP:0000558 abnormal tibia morphology skos:closeMatch HP:0002992 Abnormality of tibia morphology semapv:LexicalMatching 19 | MP:0001259 abnormal body weight skos:closeMatch HP:0004323 Abnormality of body weight semapv:LexicalMatching 20 | MP:0001260 increased body weight skos:closeMatch HP:0004324 Increased body weight semapv:LexicalMatching 21 | MP:0001262 decreased body weight skos:closeMatch HP:0004325 Decreased body weight semapv:LexicalMatching 22 | MP:0002764 short tibia skos:closeMatch HP:0005736 Short tibia semapv:LexicalMatching 23 | MP:0004357 long tibia skos:closeMatch HP:0010504 Increased length of the tibia semapv:LexicalMatching 24 | -------------------------------------------------------------------------------- /mappings/mp_hp_owt_impc.sssom.tsv: -------------------------------------------------------------------------------- 1 | # creator_id: orcid:0000-0002-2232-0967 2 | # curie_map: 3 | # HP: http://purl.obolibrary.org/obo/HP_ 4 | # MP: http://purl.obolibrary.org/obo/MP_ 5 | # owl: http://www.w3.org/2002/07/owl# 6 | # rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# 7 | # rdfs: http://www.w3.org/2000/01/rdf-schema# 8 | # skos: http://www.w3.org/2004/02/skos/core# 9 | # sssom: https://w3id.org/sssom/ 10 | # orcid: https://orcid.org/ 11 | # obo: http://purl.obolibrary.org/obo/ 12 | # semapv: https://w3id.org/semapv/vocab/ 13 | # license: https://creativecommons.org/publicdomain/zero/1.0/ 14 | # mapping_provider: https://www.mousephenotype.org 15 | # mapping_set_description: 'The IMPC Mouse Morphology Mappings: Organ Weight Test' 16 | # mapping_set_id: https://w3id.org/sssom/commons/mouse-human/mappings/mp_hp_owt_impc.sssom.tsv 17 | subject_id subject_label predicate_id object_id object_label mapping_justification 18 | MP:0001259 abnormal body weight skos:exactMatch HP:0004323 Abnormality of body weight semapv:LexicalMatching 19 | MP:0001260 increased body weight skos:exactMatch HP:0004324 Increased body weight semapv:LexicalMatching 20 | MP:0001262 decreased body weight skos:exactMatch HP:0004325 Decreased body weight semapv:LexicalMatching 21 | MP:0002707 abnormal kidney weight skos:closeMatch HP:0000077 Abnormality of the kidney semapv:LogicalReasoning 22 | MP:0002707 abnormal kidney weight skos:closeMatch HP:0000077 Abnormality of the kidney semapv:LogicalReasoning 23 | MP:0002981 increased liver weight skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 24 | MP:0003402 decreased liver weight skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 25 | MP:0003917 increased kidney weight skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 26 | MP:0003917 increased kidney weight skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 27 | MP:0003918 decreased kidney weight skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 28 | MP:0003918 decreased kidney weight skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 29 | MP:0004847 abnormal liver weight skos:closeMatch HP:0001392 Abnormality of the liver semapv:LogicalReasoning 30 | MP:0004850 abnormal testis weight skos:closeMatch HP:0000035 Abnormal testis morphology semapv:LogicalReasoning 31 | MP:0004850 abnormal testis weight skos:closeMatch HP:0000035 Abnormal testis morphology semapv:LogicalReasoning 32 | MP:0004851 increased testis weight skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 33 | MP:0004851 increased testis weight skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 34 | MP:0004852 decreased testis weight skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 35 | MP:0004852 decreased testis weight skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 36 | MP:0004908 abnormal seminal vesicle weight skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 37 | MP:0004909 increased seminal vesicle weight skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 38 | MP:0004910 decreased seminal vesicle weight skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 39 | MP:0004927 abnormal epididymis weight skos:closeMatch HP:0009714 Abnormality of the epididymis semapv:LogicalReasoning 40 | MP:0004928 increased epididymis weight skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 41 | MP:0004929 decreased epididymis weight skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 42 | MP:0004951 abnormal spleen weight skos:narrowMatch HP:0001743 Abnormality of the spleen semapv:LogicalReasoning 43 | MP:0004952 increased spleen weight skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 44 | MP:0004953 decreased spleen weight skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 45 | MP:0005629 abnormal lung weight skos:closeMatch HP:0002088 Abnormal lung morphology semapv:LogicalReasoning 46 | MP:0005629 abnormal lung weight skos:closeMatch HP:0002088 Abnormal lung morphology semapv:LogicalReasoning 47 | MP:0005630 increased lung weight skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 48 | MP:0005630 increased lung weight skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 49 | MP:0005631 decreased lung weight skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 50 | MP:0005631 decreased lung weight skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 51 | -------------------------------------------------------------------------------- /mappings/mp_hp_pat_impc.sssom.tsv: -------------------------------------------------------------------------------- 1 | # creator_id: orcid:0000-0002-2232-0967 2 | # curie_map: 3 | # HP: http://purl.obolibrary.org/obo/HP_ 4 | # MP: http://purl.obolibrary.org/obo/MP_ 5 | # owl: http://www.w3.org/2002/07/owl# 6 | # rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# 7 | # rdfs: http://www.w3.org/2000/01/rdf-schema# 8 | # skos: http://www.w3.org/2004/02/skos/core# 9 | # sssom: https://w3id.org/sssom/ 10 | # orcid: https://orcid.org/ 11 | # obo: http://purl.obolibrary.org/obo/ 12 | # semapv: https://w3id.org/semapv/vocab/ 13 | # license: https://creativecommons.org/publicdomain/zero/1.0/ 14 | # mapping_provider: https://www.mousephenotype.org 15 | # mapping_set_description: 'The IMPC Mouse Morphology Mappings: Gross Pathology & Tissue 16 | # Collection Test (Phenotype)' 17 | # mapping_set_id: https://w3id.org/sssom/commons/mouse-human/mappings/mp_hp_pat_impc.sssom.tsv 18 | subject_id subject_label predicate_id object_id object_label mapping_justification 19 | MP:0000005 increased brown fat amount skos:closeMatch HP:0000468 Increased adipose tissue around neck semapv:LogicalReasoning 20 | MP:0000017 big ears skos:closeMatch HP:0000400 Macrotia semapv:LogicalReasoning 21 | MP:0000018 small ears skos:closeMatch HP:0008551 Microtia semapv:LogicalReasoning 22 | MP:0000157 abnormal sternum morphology skos:closeMatch HP:0000766 Abnormality of the sternum semapv:LexicalMatching 23 | MP:0000158 absent sternum skos:closeMatch HP:0010308 Asternia semapv:LogicalReasoning 24 | MP:0000266 abnormal heart morphology skos:closeMatch HP:0001654 Abnormal heart morphology semapv:LexicalMatching 25 | MP:0000274 enlarged heart skos:closeMatch HP:0001640 Cardiomegaly semapv:LogicalReasoning 26 | MP:0000467 abnormal esophagus morphology skos:closeMatch HP:0002031 Abnormal esophagus morphology semapv:LexicalMatching 27 | MP:0000470 abnormal stomach morphology skos:closeMatch HP:0002577 Abnormality of the stomach semapv:LogicalReasoning 28 | MP:0000492 abnormal rectum morphology skos:closeMatch HP:0002034 Abnormality of the rectum semapv:LexicalMatching 29 | MP:0000493 rectal prolapse skos:closeMatch HP:0002035 Rectal prolapse semapv:LexicalMatching 30 | MP:0000494 abnormal cecum morphology skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 31 | MP:0000495 abnormal colon morphology skos:closeMatch HP:0002250 Abnormal large intestine morphology semapv:LexicalMatching 32 | MP:0000498 absent jejunum skos:closeMatch HP:0005235 Jejunal atresia semapv:LogicalReasoning 33 | MP:0000499 absent ileum skos:closeMatch HP:0011102 Ileal atresia semapv:LogicalReasoning 34 | MP:0000538 abnormal urinary bladder morphology skos:closeMatch HP:0025487 Abnormality of bladder morphology semapv:LexicalMatching 35 | MP:0000558 abnormal tibia morphology skos:closeMatch HP:0002992 Abnormality of tibia morphology semapv:LexicalMatching 36 | MP:0000559 abnormal femur morphology skos:closeMatch HP:0002823 Abnormality of femur morphology semapv:LexicalMatching 37 | MP:0000598 abnormal liver morphology skos:closeMatch HP:0410042 Abnormal liver morphology semapv:LexicalMatching 38 | MP:0000599 enlarged liver skos:closeMatch HP:0002240 Hepatomegaly semapv:LogicalReasoning 39 | MP:0000601 small liver skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 40 | MP:0000613 abnormal salivary gland morphology skos:closeMatch HP:0010286 Abnormal salivary gland morphology semapv:LexicalMatching 41 | MP:0000614 absent salivary gland skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 42 | MP:0000618 small salivary gland skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 43 | MP:0000627 abnormal mammary gland morphology skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 44 | MP:0000629 absent mammary gland skos:closeMatch HP:0100783 Breast aplasia semapv:LogicalReasoning 45 | MP:0000633 abnormal pituitary gland morphology skos:closeMatch HP:0012503 Abnormality of the pituitary gland semapv:LexicalMatching 46 | MP:0000636 enlarged pituitary gland skos:closeMatch HP:0012505 Enlarged pituitary gland semapv:LexicalMatching 47 | MP:0000639 abnormal adrenal gland morphology skos:closeMatch HP:0011732 Abnormality of adrenal morphology semapv:LexicalMatching 48 | MP:0000642 enlarged adrenal glands skos:closeMatch HP:0008221 Adrenal hyperplasia semapv:LexicalMatching 49 | MP:0000681 abnormal thyroid gland morphology skos:closeMatch HP:0011772 Abnormality of thyroid morphology semapv:LexicalMatching 50 | MP:0000689 abnormal spleen morphology skos:closeMatch HP:0025408 Abnormal spleen morphology semapv:LexicalMatching 51 | MP:0000690 absent spleen skos:closeMatch HP:0001746 Asplenia semapv:LogicalReasoning 52 | MP:0000691 enlarged spleen skos:closeMatch HP:0001744 Splenomegaly semapv:LogicalReasoning 53 | MP:0000692 small spleen skos:closeMatch HP:0006270 Hypoplastic spleen semapv:LogicalReasoning 54 | MP:0000702 enlarged lymph nodes skos:closeMatch HP:0002716 Lymphadenopathy semapv:LogicalReasoning 55 | MP:0000703 abnormal thymus morphology skos:closeMatch HP:0000777 Abnormality of the thymus semapv:LexicalMatching 56 | MP:0000705 athymia skos:closeMatch HP:0005359 Aplasia of the thymus semapv:LogicalReasoning 57 | MP:0000706 small thymus skos:closeMatch HP:0000778 Hypoplasia of the thymus semapv:LogicalReasoning 58 | MP:0000709 enlarged thymus skos:closeMatch HP:0010516 Thymus hyperplasia semapv:LogicalReasoning 59 | MP:0000759 abnormal skeletal muscle morphology skos:closeMatch HP:0011805 Abnormal skeletal muscle morphology semapv:LexicalMatching 60 | MP:0000762 abnormal tongue morphology skos:closeMatch HP:0030809 Abnormal tongue morphology semapv:LexicalMatching 61 | MP:0000774 decreased brain size skos:closeMatch HP:0007058 Generalized cerebral atrophy/hypoplasia semapv:LogicalReasoning 62 | MP:000095 abnormal spinal cord morphology skos:closeMatch HP:0002143 Abnormality of the spinal cord semapv:LexicalMatching 63 | MP:0001092 abnormal trigeminal ganglion morphology skos:closeMatch HP:0410016 Abnormality of cranial ganglion semapv:LexicalMatching 64 | MP:0001093 small trigeminal ganglion skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 65 | MP:0001095 enlarged trigeminal ganglion skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 66 | MP:0001102 abnormal uterus morphology skos:closeMatch HP:0031105 Abnormal uterus morphology semapv:LexicalMatching 67 | MP:0001126 abnormal ovary morphology skos:closeMatch HP:0031065 Abnormal ovarian morphology semapv:LexicalMatching 68 | MP:0001127 small ovary skos:closeMatch HP:0009724 Hypoplasia of the ovary semapv:LogicalReasoning 69 | MP:0001146 abnormal testis morphology skos:closeMatch HP:0000035 Abnormal testis morphology semapv:LexicalMatching 70 | MP:0001147 small testis skos:closeMatch HP:0008734 Decreased testicular size semapv:LogicalReasoning 71 | MP:0001148 enlarged testes skos:closeMatch HP:0000053 Macroorchidism semapv:LogicalReasoning 72 | MP:0001157 small seminal vesicle skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 73 | MP:0001158 abnormal prostate gland morphology skos:closeMatch HP:0008775 Abnormal prostate morphology semapv:LexicalMatching 74 | MP:0001159 absent prostate gland skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 75 | MP:0001175 abnormal lung morphology skos:closeMatch HP:0002088 Abnormal lung morphology semapv:LexicalMatching 76 | MP:0001181 absent lung skos:closeMatch HP:0006703 Aplasia/Hypoplasia of the lungs semapv:LogicalReasoning 77 | MP:0001192 scaly skin skos:closeMatch HP:0040189 Scaling skin semapv:LexicalMatching 78 | MP:0001199 thin skin skos:closeMatch HP:0000963 Thin skin semapv:LexicalMatching 79 | MP:0001200 thick skin skos:closeMatch HP:0001072 Thickened skin semapv:LexicalMatching 80 | MP:0001211 wrinkled skin skos:closeMatch HP:0007392 Excessive wrinkled skin semapv:LexicalMatching 81 | MP:0001293 anophthalmia skos:closeMatch HP:0000528 Anophthalmia semapv:LexicalMatching 82 | MP:0001296 macrophthalmia skos:closeMatch HP:0001090 Abnormally large globe semapv:LogicalReasoning 83 | MP:0001297 microphthalmia skos:exactMatch HP:0000568 Microphthalmia semapv:LexicalMatching 84 | MP:0001330 abnormal optic nerve morphology skos:closeMatch HP:0000587 Abnormality of the optic nerve semapv:LogicalReasoning 85 | MP:0001333 absent optic nerve skos:closeMatch HP:0012521 Optic nerve aplasia semapv:LogicalReasoning 86 | MP:0001782 increased white adipose tissue amount skos:closeMatch HP:0008993 Increased intraabdominal fat semapv:LogicalReasoning 87 | MP:0001783 decreased white adipose tissue amount skos:closeMatch HP:0025128 Reduced intraabdominal adipose tissue semapv:LogicalReasoning 88 | MP:0001891 hydroencephaly skos:closeMatch HP:0000238 Hydrocephalus semapv:LexicalMatching 89 | MP:0001944 abnormal pancreas morphology skos:closeMatch HP:0012090 Abnormal pancreas morphology semapv:LexicalMatching 90 | MP:0002059 abnormal seminal vesicle morphology skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 91 | MP:0002060 abnormal skin morphology skos:closeMatch HP:0011121 Abnormality of skin morphology semapv:LexicalMatching 92 | MP:0002092 abnormal eye morphology skos:closeMatch HP:0012372 Abnormal eye morphology semapv:LexicalMatching 93 | MP:0002102 abnormal ear morphology skos:closeMatch HP:0031703 Abnormal ear morphology semapv:LexicalMatching 94 | MP:0002135 abnormal kidney morphology skos:closeMatch HP:0012210 Abnormal renal morphology semapv:LexicalMatching 95 | MP:0002152 abnormal brain morphology skos:exactMatch HP:0012443 Abnormality of brain morphology semapv:LexicalMatching 96 | MP:0002188 small heart skos:closeMatch HP:0001961 Hypoplastic heart semapv:LogicalReasoning 97 | MP:0002217 small lymph nodes skos:closeMatch HP:0002732 Lymph node hypoplasia semapv:LogicalReasoning 98 | MP:0002219 decreased lymph node number skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 99 | MP:0002237 abnormal nasal cavity morphology skos:closeMatch HP:0010640 Abnormality of the nasal cavity semapv:LexicalMatching 100 | MP:0002282 abnormal trachea morphology skos:closeMatch HP:0002778 Abnormal trachea morphology semapv:LexicalMatching 101 | MP:0002286 cryptorchism skos:closeMatch HP:0000028 Cryptorchidism semapv:LexicalMatching 102 | MP:0002339 abnormal lymph node morphology skos:closeMatch HP:0002733 Abnormality of the lymph nodes semapv:LexicalMatching 103 | MP:0002397 abnormal bone marrow morphology skos:closeMatch HP:0005561 Abnormality of bone marrow cell morphology semapv:LexicalMatching 104 | MP:0002581 abnormal ileum morphology skos:closeMatch HP:0001549 Abnormal ileum morphology semapv:LogicalReasoning 105 | MP:0002631 abnormal epididymis morphology skos:closeMatch HP:0009714 Abnormality of the epididymis semapv:LexicalMatching 106 | MP:0002637 small uterus skos:closeMatch HP:0000013 Hypoplasia of the uterus semapv:LogicalReasoning 107 | MP:0002651 abnormal sciatic nerve morphology skos:closeMatch HP:0045010 Abnormality of peripheral nerves semapv:LogicalReasoning 108 | MP:0002689 abnormal molar morphology skos:closeMatch HP:0011070 Abnormality of molar morphology semapv:LexicalMatching 109 | MP:0002691 small stomach skos:closeMatch HP:0100841 Microgastria semapv:LogicalReasoning 110 | MP:0002728 absent tibia skos:closeMatch HP:0009556 Absent tibia semapv:LexicalMatching 111 | MP:0002731 megacolon skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 112 | MP:0002764 short tibia skos:closeMatch HP:0005736 Short tibia semapv:LexicalMatching 113 | MP:0002768 small adrenal glands skos:closeMatch HP:0000835 Adrenal hypoplasia semapv:LexicalMatching 114 | MP:0002774 small prostate gland skos:closeMatch HP:0008687 Hypoplasia of the prostate semapv:LogicalReasoning 115 | MP:0002932 abnormal joint morphology skos:closeMatch HP:0001367 Abnormal joint morphology semapv:LexicalMatching 116 | MP:0002951 small thyroid gland skos:closeMatch HP:0005990 Thyroid hypoplasia semapv:LogicalReasoning 117 | MP:0002970 abnormal white adipose tissue morphology skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 118 | MP:0002971 abnormal brown fat morphology skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 119 | MP:0002989 small kidney skos:closeMatch HP:0000089 Renal hypoplasia semapv:LogicalReasoning 120 | MP:0002997 enlarged seminal vesicle skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 121 | MP:0003068 enlarged kidney skos:closeMatch HP:0000105 Enlarged kidney semapv:LexicalMatching 122 | MP:0003109 short femur skos:closeMatch HP:0003097 Short femur semapv:LexicalMatching 123 | MP:0003189 fused joints skos:closeMatch HP:0100240 Synostosis of joints semapv:LogicalReasoning 124 | MP:0003250 absent gall bladder skos:closeMatch HP:0011467 Absent gallbladder semapv:LexicalMatching 125 | MP:0003271 abnormal duodenum morphology skos:closeMatch HP:0030992 Abnormality of the duodenum semapv:LexicalMatching 126 | MP:0003294 intussusception skos:closeMatch HP:0002576 Intussusception semapv:LogicalReasoning 127 | MP:0003296 microcolon skos:closeMatch HP:0004388 Microcolon semapv:LexicalMatching 128 | MP:0003318 rectoperineal fistula skos:closeMatch HP:0004792 Rectoperineal fistula semapv:LexicalMatching 129 | MP:0003320 rectovaginal fistula skos:closeMatch HP:0000143 Rectovaginal fistula semapv:LexicalMatching 130 | MP:0003321 tracheoesophageal fistula skos:closeMatch HP:0002575 Tracheoesophageal fistula semapv:LexicalMatching 131 | MP:0003450 enlarged pancreas skos:closeMatch HP:0006277 Pancreatic hyperplasia semapv:LogicalReasoning 132 | MP:0003558 absent uterus skos:closeMatch HP:0000151 Aplasia of the uterus semapv:LogicalReasoning 133 | MP:0003578 absent ovary skos:closeMatch HP:0010463 Aplasia of the ovary semapv:LogicalReasoning 134 | MP:0003604 single kidney skos:closeMatch HP:0000122 Unilateral renal agenesis semapv:LogicalReasoning 135 | MP:0003641 small lung skos:closeMatch HP:0006703 Aplasia/Hypoplasia of the lungs semapv:LogicalReasoning 136 | MP:0003642 absent seminal vesicle skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 137 | MP:0003655 absent pancreas skos:closeMatch HP:0100801 Pancreatic aplasia semapv:LogicalReasoning 138 | MP:0003678 absent ear lobes skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 139 | MP:0003795 abnormal bone structure skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 140 | MP:0003883 enlarged stomach skos:closeMatch HP:0005207 Gastic hypertrophy semapv:LogicalReasoning 141 | MP:0004002 abnormal jejunum morphology skos:closeMatch HP:0005265 Abnormality of the jejunum semapv:LogicalReasoning 142 | MP:0004247 small pancreas skos:closeMatch HP:0002594 Pancreatic hypoplasia semapv:LogicalReasoning 143 | MP:0004320 split sternum skos:closeMatch HP:0010309 Bifid sternum semapv:LogicalReasoning 144 | MP:0004321 short sternum skos:closeMatch HP:0000879 Short sternum semapv:LexicalMatching 145 | MP:0004348 long femur skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 146 | MP:0004349 absent femur skos:closeMatch HP:0012274 Femoral aplasia semapv:LogicalReasoning 147 | MP:0004357 long tibia skos:closeMatch HP:0010504 Increased length of the tibia semapv:LexicalMatching 148 | MP:0004545 enlarged esophagus skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 149 | MP:0004549 small trachea skos:closeMatch HP:0100682 Tracheal atresia semapv:LogicalReasoning 150 | MP:0004727 absent epididymus skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 151 | MP:0004818 increased skeletal muscle mass skos:closeMatch HP:0003712 Skeletal muscle hypertrophy semapv:LogicalReasoning 152 | MP:0004819 decreased skeletal muscle mass skos:closeMatch HP:0001460 Aplasia/Hypoplasia involving the skeletal musculature semapv:LogicalReasoning 153 | MP:0004832 enlarged ovary skos:closeMatch HP:0100879 Enlarged ovaries semapv:LexicalMatching 154 | MP:0004882 enlarged lung skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 155 | MP:0004906 enlarged uterus skos:closeMatch HP:0100878 Enlarged uterus semapv:LexicalMatching 156 | MP:0004930 small epididymus skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 157 | MP:0004931 enlarged epididymus skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 158 | MP:0004958 enlarged prostate gland skos:closeMatch HP:0008711 Benign prostatic hyperplasia semapv:LogicalReasoning 159 | MP:0005084 abnormal gall bladder morphology skos:closeMatch HP:0012437 Abnormal gallbladder morphology semapv:LexicalMatching 160 | MP:0005238 increased brain size skos:closeMatch HP:0001355 Megalencephaly semapv:LogicalReasoning 161 | MP:0005313 absent adrenal gland skos:closeMatch HP:0011743 Adrenal gland agenesis semapv:LexicalMatching 162 | MP:0005314 absent thyroid gland skos:closeMatch HP:0008191 Thyroid agenesis semapv:LogicalReasoning 163 | MP:0005315 absent pituitary gland skos:closeMatch HP:0410279 Atrophic parotid gland semapv:LogicalReasoning 164 | MP:0005355 enlarged thyroid gland skos:closeMatch HP:0008249 Thyroid hyperplasia semapv:LogicalReasoning 165 | MP:0005358 anbornormal incisor morphology skos:closeMatch HP:0011063 Abnormality of incisor morphology semapv:LexicalMatching 166 | MP:0005361 small pituitary gland skos:closeMatch HP:0012506 Small pituitary gland semapv:LexicalMatching 167 | MP:0005675 small gall bladder skos:closeMatch HP:0005233 Hypoplasia of the gallbladder semapv:LogicalReasoning 168 | MP:0006065 abnormal heart position or orientation skos:closeMatch HP:0004307 Abnormal anatomic location of the heart semapv:LogicalReasoning 169 | MP:0006221 optic nerve hypoplasia skos:closeMatch HP:0000609 Optic nerve hypoplasia semapv:LexicalMatching 170 | MP:0006415 absent testes skos:closeMatch HP:0010469 Absent testis semapv:LexicalMatching 171 | MP:0007180 decreased brown fat amount skos:closeMatch HP:0005995 Decreased adipose tissue around neck semapv:LogicalReasoning 172 | MP:0008024 absent lymph nodes skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 173 | MP:0008528 polycystic kidney skos:closeMatch HP:0000113 Polycystic kidney dysplasia semapv:LexicalMatching 174 | MP:0008529 enlarged optic nerve skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 175 | MP:0008725 enlarged heart atrium skos:closeMatch HP:0031295 Left atrial enlargement semapv:LogicalReasoning 176 | MP:0008725 enlarged heart atrium skos:closeMatch HP:0030718 Right atrial enlargement semapv:LogicalReasoning 177 | MP:0008844 decreased subcutaneous adipose tissue amount skos:closeMatch HP:0003758 Reduced subcutaneous fat semapv:LogicalReasoning 178 | MP:0009000 absent cecum skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 179 | MP:0009084 blind uterus skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 180 | MP:0009252 absent urinary bladder skos:closeMatch HP:0010476 Aplasia/Hypoplasia of the bladder semapv:LogicalReasoning 181 | MP:0009342 enlarged gall bladder skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 182 | MP:0009476 enlarged cecum skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 183 | MP:0009477 small cecum skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 184 | MP:0009483 enlarged ileum skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 185 | MP:0009509 absent rectum skos:closeMatch HP:0025023 Rectal atresia semapv:LogicalReasoning 186 | MP:0009516 enlarged salivary gland skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 187 | MP:0009552 urinary bladder obstruction skos:closeMatch HP:0041047 Bladder outlet obstruction semapv:LexicalMatching 188 | MP:0009709 hydrometra skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 189 | MP:0009721 supernumerary mammary glands skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 190 | MP:0009905 absent tongue skos:closeMatch HP:0010295 Aplasia/Hypoplasia of the tongue semapv:LogicalReasoning 191 | MP:0009906 increased tongue size skos:closeMatch HP:0000158 Macroglossia semapv:LogicalReasoning 192 | MP:0009907 decreased tongue size skos:closeMatch HP:0000171 Microglossia semapv:LogicalReasoning 193 | MP:0010880 small esophagus skos:closeMatch HP:0002032 Esophageal atresia semapv:LogicalReasoning 194 | MP:0010934 increased subcutaneous adipose tissue amount skos:closeMatch HP:0009003 Increased subcutaneous truncal adipose tissue semapv:LogicalReasoning 195 | MP:0011156 abnormal hypodermis fat layer morphology skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 196 | MP:0011503 distended jejunum skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 197 | MP:0011625 cystolithiasis skos:closeMatch HP:0010474 Bladder stones semapv:LogicalReasoning 198 | MP:0011874 enlarged urinary bladder skos:closeMatch HP:0008635 Hypertrophy of the urinary bladder semapv:LogicalReasoning 199 | MP:0011875 absent stomach skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 200 | MP:0011877 absent liver skos:closeMatch HP:0100839 Hepatic agenesis semapv:LogicalReasoning 201 | MP:0011880 absent duodenum skos:closeMatch HP:0002247 Duodenal atresia semapv:LogicalReasoning 202 | MP:0011882 enlarged duodenum skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 203 | MP:0011884 absent colon skos:closeMatch HP:0500027 Aplastic colon semapv:LogicalReasoning 204 | MP:0012279 wide sternum skos:closeMatch sssom:NoTermFound No Term Found semapv:ManualMappingCuration 205 | MP:0012672 enlarged trachea skos:closeMatch HP:0010778 Tracheomegaly semapv:LogicalReasoning 206 | MP:0013129 abnormal tooth colour skos:closeMatch HP:0011073 Abnormality of dental color semapv:LexicalMatching 207 | -------------------------------------------------------------------------------- /mappings/mp_hp_xry_impc.sssom.tsv: -------------------------------------------------------------------------------- 1 | # creator_id: orcid:0000-0002-2232-0967 2 | # curie_map: 3 | # HP: http://purl.obolibrary.org/obo/HP_ 4 | # MP: http://purl.obolibrary.org/obo/MP_ 5 | # owl: http://www.w3.org/2002/07/owl# 6 | # rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# 7 | # rdfs: http://www.w3.org/2000/01/rdf-schema# 8 | # skos: http://www.w3.org/2004/02/skos/core# 9 | # sssom: https://w3id.org/sssom/ 10 | # orcid: https://orcid.org/ 11 | # obo: http://purl.obolibrary.org/obo/ 12 | # semapv: https://w3id.org/semapv/vocab/ 13 | # license: https://creativecommons.org/publicdomain/zero/1.0/ 14 | # mapping_provider: https://www.mousephenotype.org 15 | # mapping_set_description: 'The IMPC Mouse Morphology Mappings: X-ray Test' 16 | # mapping_set_id: https://w3id.org/sssom/commons/mouse-human/mappings/mp_hp_xry_impc.sssom.tsv 17 | subject_id subject_label predicate_id object_id object_label mapping_justification 18 | MP:0000137 abnormal vertebrae morphology skos:closeMatch HP:0003468 Abnormal vertebral morphology semapv:LexicalMatching 19 | MP:0000149 abnormal scapula morphology skos:closeMatch HP:0000782 Abnormality of the scapula semapv:LexicalMatching 20 | MP:0000150 abnormal rib morphology skos:closeMatch HP:0001547 Abnormality of the rib cage semapv:LogicalReasoning 21 | MP:0000154 rib fusion skos:closeMatch HP:0000902 Rib fusion semapv:LexicalMatching 22 | MP:0000160 kyphosis skos:closeMatch HP:0002808 Kyphosis semapv:LexicalMatching 23 | MP:0000161 scoliosis skos:closeMatch HP:0002650 Scoliosis semapv:LexicalMatching 24 | MP:0000162 lordosis skos:closeMatch HP:0002938 Lumbar hyperlordosis semapv:LogicalReasoning 25 | MP:0000438 abnormal cranium morphology skos:closeMatch HP:0002648 Abnormality of calvarial morphology semapv:LexicalMatching 26 | MP:0000455 abnormal maxilla morphology skos:closeMatch HP:0000326 Abnormality of the maxilla semapv:LexicalMatching 27 | MP:0000458 abnormal mandible morphology skos:closeMatch HP:0000277 Abnormality of the mandible semapv:LexicalMatching 28 | MP:0000480 increased rib number skos:closeMatch sssom:NoTermFound No term found semapv:ManualMappingCuration 29 | MP:0000480 increased rib number skos:closeMatch sssom:NoTermFound No term found semapv:ManualMappingCuration 30 | MP:0000552 abnormal radius morphology skos:closeMatch HP:0045009 Abnormal morphology of the radius semapv:LexicalMatching 31 | MP:0000558 abnormal tibia morphology skos:closeMatch HP:0002992 Abnormality of tibia morphology semapv:LexicalMatching 32 | MP:0000559 abnormal femur morphology skos:closeMatch HP:0002823 Abnormality of femur morphology semapv:LexicalMatching 33 | MP:0000562 polydactyly skos:closeMatch HP:0010442 Polydactyly semapv:LexicalMatching 34 | MP:0000564 syndactyly skos:closeMatch HP:0001159 Syndactyly semapv:LexicalMatching 35 | MP:0000565 oligodactyly skos:closeMatch HP:0012165 Oligodactyly semapv:LexicalMatching 36 | MP:0001539 decreased caudal vertebrae number skos:closeMatch HP:0030305 Decreased number of vertebrae semapv:LexicalMatching 37 | MP:0002100 abnormal tooth morphology skos:closeMatch HP:0006482 Abnormality of dental morphology semapv:LogicalReasoning 38 | MP:0002110 abnormal digit morphology skos:closeMatch HP:0011297 Abnormal digit morphology semapv:LexicalMatching 39 | MP:0002187 abnormal fibula morphology skos:closeMatch HP:0002991 Abnormality of fibula morphology semapv:LexicalMatching 40 | MP:0002544 brachydactyly skos:closeMatch HP:0001156 Brachydactyly semapv:LexicalMatching 41 | MP:0002759 abnormal caudal vertebrae morphology skos:closeMatch HP:0003468 Abnormal vertebral morphology semapv:LexicalMatching 42 | MP:0002764 short tibia skos:closeMatch HP:0005736 Short tibia semapv:LexicalMatching 43 | MP:0002932 abnormal joint morphology skos:closeMatch HP:0001367 Abnormal joint morphology semapv:LexicalMatching 44 | MP:0003036 vertebral transformation skos:closeMatch HP:0003468 Abnormal vertebral morphology semapv:LogicalReasoning 45 | MP:0003047 abnormal thoracic vertebrae morphology skos:closeMatch HP:0003468 Abnormal vertebral morphology semapv:LexicalMatching 46 | MP:0003048 abnormal cervical vertebrae morphology skos:closeMatch HP:0003468 Abnormal vertebral morphology semapv:LexicalMatching 47 | MP:0003049 abnormal lumbar vertebrae morphology skos:closeMatch HP:0003468 Abnormal vertebral morphology semapv:LexicalMatching 48 | MP:0003345 decreased rib number skos:closeMatch HP:0000921 Missing ribs semapv:LogicalReasoning 49 | MP:0003345 decreased rib number skos:closeMatch HP:0000921 Missing ribs semapv:LogicalReasoning 50 | MP:0004083 polysyndactyly skos:closeMatch HP:0005817 Postaxial polysyndactyly of foot semapv:LogicalReasoning 51 | MP:0004174 abnormal spine curvature skos:closeMatch HP:0010674 Abnormality of the curvature of the vertebral column semapv:LogicalReasoning 52 | MP:0004357 long tibia skos:closeMatch HP:0002992 Abnormality of tibia morphology semapv:LexicalMatching 53 | MP:0004509 abnormal pelvic girdle bone morphology skos:closeMatch HP:0002644 Abnormality of pelvic girdle bone morphology semapv:LexicalMatching 54 | MP:0004599 abnormal vertebral arch morphology skos:closeMatch HP:0008438 Vertebral arch anomaly semapv:LexicalMatching 55 | MP:0004599 abnormal vertebral arch morphology skos:closeMatch HP:0008438 Vertebral arch anomaly semapv:LexicalMatching 56 | MP:0004599 abnormal vertebral arch morphology skos:closeMatch HP:0008438 Vertebral arch anomaly semapv:LexicalMatching 57 | MP:0004599 abnormal vertebral arch morphology skos:closeMatch HP:0008438 Vertebral arch anomaly semapv:LexicalMatching 58 | MP:0004599 abnormal vertebral arch morphology skos:closeMatch HP:0008438 Vertebral arch anomaly semapv:LexicalMatching 59 | MP:0004609 vertebral fusion skos:closeMatch HP:0002948 Vertebral fusion semapv:LexicalMatching 60 | MP:0004613 fusion of vertebral arches skos:closeMatch HP:0002948 Vertebral fusion semapv:LexicalMatching 61 | MP:0004646 decreased cervical vertebrae number skos:closeMatch HP:0030305 Decreased number of vertebrae semapv:LexicalMatching 62 | MP:0004647 decreased lumbar vertebrae number skos:closeMatch HP:0030305 Decreased number of vertebrae semapv:LexicalMatching 63 | MP:0004648 decreased thoracic vertebrae number skos:closeMatch HP:0030305 Decreased number of vertebrae semapv:LexicalMatching 64 | MP:0004649 decreased sacral vertebrae number skos:closeMatch HP:0030305 Decreased number of vertebrae semapv:LexicalMatching 65 | MP:0004650 increased lumbar vertebrae number skos:closeMatch HP:0002946 Supernumerary vertebrae semapv:LogicalReasoning 66 | MP:0004651 increased thoracic vertebrae number skos:closeMatch HP:0002946 Supernumerary vertebrae semapv:LogicalReasoning 67 | MP:0005108 abnormal ulna morphology skos:closeMatch HP:0040071 Abnormal morphology of ulna semapv:LexicalMatching 68 | MP:0005270 abnormal zygomatic bone morphology skos:exactMatch HP:0010668 Abnormality of the zygomatic bone semapv:LexicalMatching 69 | MP:0005296 abnormal humerus morphology skos:closeMatch HP:0031095 Abnormal humerus morphology semapv:LexicalMatching 70 | MP:0005298 abnormal clavicle morphology skos:closeMatch HP:0000889 Abnormality of the clavicle semapv:LexicalMatching 71 | MP:0010099 abnormal thoracic cage shape skos:closeMatch HP:0001547 Abnormality of the rib cage semapv:LogicalReasoning 72 | MP:0010100 increased cervical vertebrae number skos:closeMatch HP:0002946 Supernumerary vertebrae semapv:LogicalReasoning 73 | MP:0010101 increased sacral vertebrae number skos:closeMatch HP:0002946 Supernumerary vertebrae semapv:LogicalReasoning 74 | MP:0010102 increased caudal vertebrae number skos:closeMatch HP:0002946 Supernumerary vertebrae semapv:LogicalReasoning 75 | -------------------------------------------------------------------------------- /mappings/ordo_mp_pistoia.sssom.tsv: -------------------------------------------------------------------------------- 1 | # curie_map: 2 | # MP: http://purl.obolibrary.org/obo/MP_ 3 | # orphanet.ordo: http://www.orpha.net/ORDO/Orphanet_ 4 | # owl: http://www.w3.org/2002/07/owl# 5 | # rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# 6 | # rdfs: http://www.w3.org/2000/01/rdf-schema# 7 | # skos: http://www.w3.org/2004/02/skos/core# 8 | # sssom: https://w3id.org/sssom/ 9 | # wikidata: https://www.wikidata.org/wiki/ 10 | # obo: http://purl.obolibrary.org/obo/ 11 | # semapv: https://w3id.org/semapv/vocab/ 12 | # license: https://creativecommons.org/publicdomain/zero/1.0/ 13 | # mapping_provider: https://www.pistoiaalliance.org/projects/current-projects/ontologies-mapping/ 14 | # mapping_set_description: 'The Pistoia Ontology Mappings: ordo_mp' 15 | # mapping_set_id: https://w3id.org/sssom/commons/mouse-human/mappings/ordo_mp_pistoia.sssom.tsv 16 | # object_source: obo:mp 17 | # subject_source: wikidata:Q24254958 18 | subject_id predicate_id object_id mapping_justification confidence 19 | orphanet.ordo:101023 owl:equivalentClass MP:0013545 semapv:UnspecifiedMatching 0.75 20 | orphanet.ordo:101043 owl:equivalentClass MP:0002747 semapv:UnspecifiedMatching 0.75 21 | orphanet.ordo:101063 owl:equivalentClass MP:0011252 semapv:UnspecifiedMatching 0.75 22 | orphanet.ordo:1041 owl:equivalentClass MP:0002192 semapv:UnspecifiedMatching 0.75 23 | orphanet.ordo:105 owl:equivalentClass MP:0003591 semapv:UnspecifiedMatching 0.2272725 24 | orphanet.ordo:1054 owl:equivalentClass MP:0010483 semapv:UnspecifiedMatching 0.2363625 25 | orphanet.ordo:1077 owl:equivalentClass MP:0030449 semapv:UnspecifiedMatching 0.75 26 | orphanet.ordo:1138 owl:equivalentClass MP:0013980 semapv:UnspecifiedMatching 0.2253525 27 | orphanet.ordo:1160 owl:equivalentClass MP:0012080 semapv:UnspecifiedMatching 0.75 28 | orphanet.ordo:118246 owl:equivalentClass MP:0001326 semapv:UnspecifiedMatching 0.238095 29 | orphanet.ordo:1199 owl:equivalentClass MP:0003276 semapv:UnspecifiedMatching 0.75 30 | orphanet.ordo:1203 owl:equivalentClass MP:0003272 semapv:UnspecifiedMatching 0.75 31 | orphanet.ordo:123411 owl:equivalentClass MP:0005638 semapv:UnspecifiedMatching 0.75 32 | orphanet.ordo:137914 owl:equivalentClass MP:0008970 semapv:UnspecifiedMatching 0.75 33 | orphanet.ordo:141163 owl:equivalentClass MP:0030328 semapv:UnspecifiedMatching 0.75 34 | orphanet.ordo:141229 owl:equivalentClass MP:0008797 semapv:UnspecifiedMatching 0.75 35 | orphanet.ordo:141253 owl:equivalentClass MP:0008799 semapv:UnspecifiedMatching 0.75 36 | orphanet.ordo:141269 owl:equivalentClass MP:0008798 semapv:UnspecifiedMatching 0.75 37 | orphanet.ordo:1457 owl:equivalentClass MP:0003387 semapv:UnspecifiedMatching 0.75 38 | orphanet.ordo:1463 owl:equivalentClass MP:0010409 semapv:UnspecifiedMatching 0.75 39 | orphanet.ordo:1464 owl:equivalentClass MP:0010432 semapv:UnspecifiedMatching 0.75 40 | orphanet.ordo:1531 owl:equivalentClass MP:0000081 semapv:UnspecifiedMatching 0.75 41 | orphanet.ordo:155878 owl:equivalentClass MP:0011615 semapv:UnspecifiedMatching 0.75 42 | orphanet.ordo:156207 owl:equivalentClass MP:0009906 semapv:UnspecifiedMatching 0.75 43 | orphanet.ordo:157769 owl:equivalentClass MP:0002767 semapv:UnspecifiedMatching 0.75 44 | orphanet.ordo:166415 owl:equivalentClass MP:0001496 semapv:UnspecifiedMatching 0.75 45 | orphanet.ordo:1666 owl:equivalentClass MP:0000644 semapv:UnspecifiedMatching 0.75 46 | orphanet.ordo:1671 owl:equivalentClass MP:0012710 semapv:UnspecifiedMatching 0.75 47 | orphanet.ordo:167848 owl:equivalentClass MP:0005330 semapv:UnspecifiedMatching 0.75 48 | orphanet.ordo:180139 owl:equivalentClass MP:0001121 semapv:UnspecifiedMatching 0.75 49 | orphanet.ordo:1848 owl:equivalentClass MP:0000520 semapv:UnspecifiedMatching 0.2448975 50 | orphanet.ordo:199323 owl:equivalentClass MP:0003665 semapv:UnspecifiedMatching 0.75 51 | orphanet.ordo:2014 owl:equivalentClass MP:0000111 semapv:UnspecifiedMatching 0.75 52 | orphanet.ordo:2038 owl:equivalentClass MP:0010480 semapv:UnspecifiedMatching 0.75 53 | orphanet.ordo:209 owl:equivalentClass MP:0005421 semapv:UnspecifiedMatching 0.75 54 | orphanet.ordo:211266 owl:equivalentClass MP:0006093 semapv:UnspecifiedMatching 0.22807 55 | orphanet.ordo:2130 owl:equivalentClass MP:0008985 semapv:UnspecifiedMatching 0.75 56 | orphanet.ordo:214 owl:equivalentClass MP:0020400 semapv:UnspecifiedMatching 0.75 57 | orphanet.ordo:2162 owl:equivalentClass MP:0005157 semapv:UnspecifiedMatching 0.75 58 | orphanet.ordo:216675 owl:equivalentClass MP:0004110 semapv:UnspecifiedMatching 0.2348475 59 | orphanet.ordo:217604 owl:equivalentClass MP:0002795 semapv:UnspecifiedMatching 0.75 60 | orphanet.ordo:2287 owl:equivalentClass MP:0030475 semapv:UnspecifiedMatching 0.75 61 | orphanet.ordo:2368 owl:equivalentClass MP:0000757 semapv:UnspecifiedMatching 0.75 62 | orphanet.ordo:263413 owl:equivalentClass MP:0003667 semapv:UnspecifiedMatching 0.75 63 | orphanet.ordo:263714 owl:equivalentClass MP:0004023 semapv:UnspecifiedMatching 0.226415 64 | orphanet.ordo:263746 owl:equivalentClass MP:0004023 semapv:UnspecifiedMatching 0.226415 65 | orphanet.ordo:268369 owl:equivalentClass MP:0012547 semapv:UnspecifiedMatching 0.75 66 | orphanet.ordo:268744 owl:equivalentClass MP:0012547 semapv:UnspecifiedMatching 0.75 67 | orphanet.ordo:2695 owl:equivalentClass MP:0030117 semapv:UnspecifiedMatching 0.75 68 | orphanet.ordo:2781 owl:equivalentClass MP:0000067 semapv:UnspecifiedMatching 0.75 69 | orphanet.ordo:284804 owl:equivalentClass MP:0006159 semapv:UnspecifiedMatching 0.75 70 | orphanet.ordo:2882 owl:equivalentClass MP:0010077 semapv:UnspecifiedMatching 0.75 71 | orphanet.ordo:2913 owl:equivalentClass MP:0000562 semapv:UnspecifiedMatching 0.75 72 | orphanet.ordo:306773 owl:equivalentClass MP:0005604 semapv:UnspecifiedMatching 0.75 73 | orphanet.ordo:3148 owl:equivalentClass MP:0002030 semapv:UnspecifiedMatching 0.246835 74 | orphanet.ordo:3169 owl:equivalentClass MP:0003445 semapv:UnspecifiedMatching 0.75 75 | orphanet.ordo:3190 owl:equivalentClass MP:0010449 semapv:UnspecifiedMatching 0.75 76 | orphanet.ordo:3193 owl:equivalentClass MP:0010471 semapv:UnspecifiedMatching 0.75 77 | orphanet.ordo:3280 owl:equivalentClass MP:0012545 semapv:UnspecifiedMatching 0.75 78 | orphanet.ordo:3289 owl:equivalentClass MP:0030496 semapv:UnspecifiedMatching 0.75 79 | orphanet.ordo:329931 owl:equivalentClass MP:0002743 semapv:UnspecifiedMatching 0.23077 80 | orphanet.ordo:3384 owl:equivalentClass MP:0002633 semapv:UnspecifiedMatching 0.23611 81 | orphanet.ordo:3426 owl:equivalentClass MP:0000284 semapv:UnspecifiedMatching 0.75 82 | orphanet.ordo:3427 owl:equivalentClass MP:0010427 semapv:UnspecifiedMatching 0.75 83 | orphanet.ordo:363483 owl:equivalentClass MP:0004478 semapv:UnspecifiedMatching 0.75 84 | orphanet.ordo:411709 owl:equivalentClass MP:0000520 semapv:UnspecifiedMatching 0.75 85 | orphanet.ordo:431341 owl:equivalentClass MP:0011852 semapv:UnspecifiedMatching 0.75 86 | orphanet.ordo:439167 owl:equivalentClass MP:0006372 semapv:UnspecifiedMatching 0.75 87 | orphanet.ordo:448270 owl:equivalentClass MP:0011660 semapv:UnspecifiedMatching 0.75 88 | orphanet.ordo:450 owl:equivalentClass MP:0004133 semapv:UnspecifiedMatching 0.75 89 | orphanet.ordo:46724 owl:equivalentClass MP:0010530 semapv:UnspecifiedMatching 0.75 90 | orphanet.ordo:480501 owl:equivalentClass MP:0003266 semapv:UnspecifiedMatching 0.75 91 | orphanet.ordo:521 owl:equivalentClass MP:0005481 semapv:UnspecifiedMatching 0.75 92 | orphanet.ordo:52759 owl:equivalentClass MP:0001864 semapv:UnspecifiedMatching 0.75 93 | orphanet.ordo:63260 owl:equivalentClass MP:0008784 semapv:UnspecifiedMatching 0.75 94 | orphanet.ordo:64720 owl:equivalentClass MP:0002035 semapv:UnspecifiedMatching 0.75 95 | orphanet.ordo:65681 owl:equivalentClass MP:0001144 semapv:UnspecifiedMatching 0.75 96 | orphanet.ordo:660 owl:equivalentClass MP:0003052 semapv:UnspecifiedMatching 0.75 97 | orphanet.ordo:674 owl:equivalentClass MP:0013291 semapv:UnspecifiedMatching 0.75 98 | orphanet.ordo:675 owl:equivalentClass MP:0006261 semapv:UnspecifiedMatching 0.75 99 | orphanet.ordo:69 owl:equivalentClass MP:0000604 semapv:UnspecifiedMatching 0.75 100 | orphanet.ordo:738 owl:equivalentClass MP:0005654 semapv:UnspecifiedMatching 0.75 101 | orphanet.ordo:755 owl:equivalentClass MP:0005536 semapv:UnspecifiedMatching 0.75 102 | orphanet.ordo:77 owl:equivalentClass MP:0005261 semapv:UnspecifiedMatching 0.75 103 | orphanet.ordo:780 owl:equivalentClass MP:0002036 semapv:UnspecifiedMatching 0.75 104 | orphanet.ordo:79225 owl:equivalentClass MP:0009589 semapv:UnspecifiedMatching 0.75 105 | orphanet.ordo:79364 owl:equivalentClass MP:0000414 semapv:UnspecifiedMatching 0.75 106 | orphanet.ordo:79365 owl:equivalentClass MP:0000412 semapv:UnspecifiedMatching 0.75 107 | orphanet.ordo:79383 owl:equivalentClass MP:0003390 semapv:UnspecifiedMatching 0.75 108 | orphanet.ordo:79389 owl:equivalentClass MP:0003786 semapv:UnspecifiedMatching 0.75 109 | orphanet.ordo:83463 owl:equivalentClass MP:0000018 semapv:UnspecifiedMatching 0.75 110 | orphanet.ordo:90025 owl:equivalentClass MP:0000564 semapv:UnspecifiedMatching 0.75 111 | orphanet.ordo:91414 owl:equivalentClass MP:0002013 semapv:UnspecifiedMatching 0.75 112 | orphanet.ordo:91495 owl:equivalentClass MP:0010711 semapv:UnspecifiedMatching 0.75 113 | orphanet.ordo:93 owl:equivalentClass MP:0011516 semapv:UnspecifiedMatching 0.75 114 | orphanet.ordo:93100 owl:equivalentClass MP:0003604 semapv:UnspecifiedMatching 0.2450975 115 | orphanet.ordo:93101 owl:equivalentClass MP:0003446 semapv:UnspecifiedMatching 0.75 116 | orphanet.ordo:93108 owl:equivalentClass MP:0002135 semapv:UnspecifiedMatching 0.75 117 | orphanet.ordo:93338 owl:equivalentClass MP:0004083 semapv:UnspecifiedMatching 0.75 118 | orphanet.ordo:93928 owl:equivalentClass MP:0003598 semapv:UnspecifiedMatching 0.75 119 | orphanet.ordo:93962 owl:equivalentClass MP:0030126 semapv:UnspecifiedMatching 0.75 120 | orphanet.ordo:93968 owl:equivalentClass MP:0012259 semapv:UnspecifiedMatching 0.75 121 | orphanet.ordo:93969 owl:equivalentClass MP:0009929 semapv:UnspecifiedMatching 0.75 122 | orphanet.ordo:93976 owl:equivalentClass MP:0003142 semapv:UnspecifiedMatching 0.75 123 | orphanet.ordo:95443 owl:equivalentClass MP:0000650 semapv:UnspecifiedMatching 0.75 124 | orphanet.ordo:95448 owl:equivalentClass MP:0006115 semapv:UnspecifiedMatching 0.75 125 | orphanet.ordo:95458 owl:equivalentClass MP:0006125 semapv:UnspecifiedMatching 0.75 126 | orphanet.ordo:95708 owl:equivalentClass MP:0003378 semapv:UnspecifiedMatching 0.75 127 | orphanet.ordo:95720 owl:equivalentClass MP:0003499 semapv:UnspecifiedMatching 0.75 128 | orphanet.ordo:963 owl:equivalentClass MP:0003506 semapv:UnspecifiedMatching 0.75 129 | orphanet.ordo:96321 owl:equivalentClass MP:0004025 semapv:UnspecifiedMatching 0.75 130 | orphanet.ordo:97275 owl:equivalentClass MP:0001847 semapv:UnspecifiedMatching 0.75 131 | orphanet.ordo:98282 owl:equivalentClass MP:0009440 semapv:UnspecifiedMatching 0.75 132 | orphanet.ordo:98427 owl:equivalentClass MP:0002872 semapv:UnspecifiedMatching 0.75 133 | orphanet.ordo:98575 owl:equivalentClass MP:0030166 semapv:UnspecifiedMatching 0.75 134 | orphanet.ordo:98613 owl:equivalentClass MP:0006193 semapv:UnspecifiedMatching 0.75 135 | orphanet.ordo:98653 owl:equivalentClass MP:0020486 semapv:UnspecifiedMatching 0.2325575 136 | orphanet.ordo:98691 owl:equivalentClass MP:0001389 semapv:UnspecifiedMatching 0.244185 137 | orphanet.ordo:98715 owl:equivalentClass MP:0005515 semapv:UnspecifiedMatching 0.75 138 | orphanet.ordo:98722 owl:equivalentClass MP:0010412 semapv:UnspecifiedMatching 0.2457625 139 | orphanet.ordo:98823 owl:equivalentClass MP:0005481 semapv:UnspecifiedMatching 0.2327575 140 | orphanet.ordo:98947 owl:equivalentClass MP:0010716 semapv:UnspecifiedMatching 0.2317075 141 | orphanet.ordo:99044 owl:equivalentClass MP:0011667 semapv:UnspecifiedMatching 0.22963 142 | orphanet.ordo:99047 owl:equivalentClass MP:0011669 semapv:UnspecifiedMatching 0.24 143 | orphanet.ordo:99054 owl:equivalentClass MP:0006128 semapv:UnspecifiedMatching 0.240385 144 | orphanet.ordo:99071 owl:equivalentClass MP:0010481 semapv:UnspecifiedMatching 0.2372875 145 | orphanet.ordo:99079 owl:equivalentClass MP:0004161 semapv:UnspecifiedMatching 0.75 146 | orphanet.ordo:99081 owl:equivalentClass MP:0004158 semapv:UnspecifiedMatching 0.75 147 | orphanet.ordo:99083 owl:equivalentClass MP:0010460 semapv:UnspecifiedMatching 0.75 148 | orphanet.ordo:99097 owl:equivalentClass MP:0010419 semapv:UnspecifiedMatching 0.238095 149 | orphanet.ordo:99098 owl:equivalentClass MP:0010411 semapv:UnspecifiedMatching 0.2386375 150 | orphanet.ordo:99099 owl:equivalentClass MP:0010410 semapv:UnspecifiedMatching 0.234695 151 | orphanet.ordo:99103 owl:equivalentClass MP:0010405 semapv:UnspecifiedMatching 0.23077 152 | orphanet.ordo:99104 owl:equivalentClass MP:0010407 semapv:UnspecifiedMatching 0.2302625 153 | orphanet.ordo:99105 owl:equivalentClass MP:0010408 semapv:UnspecifiedMatching 0.22973 154 | orphanet.ordo:99106 owl:equivalentClass MP:0010404 semapv:UnspecifiedMatching 0.22973 155 | orphanet.ordo:99107 owl:equivalentClass MP:0010450 semapv:UnspecifiedMatching 0.75 156 | orphanet.ordo:99867 owl:equivalentClass MP:0014127 semapv:UnspecifiedMatching 0.75 157 | -------------------------------------------------------------------------------- /mappings/pato_hp_pat_impc.sssom.tsv: -------------------------------------------------------------------------------- 1 | # comment: What is the purpose of this entire table? 2 | # creator_id: orcid:0000-0002-2232-0967 3 | # curie_map: 4 | # HP: http://purl.obolibrary.org/obo/HP_ 5 | # PATO: http://purl.obolibrary.org/obo/PATO_ 6 | # owl: http://www.w3.org/2002/07/owl# 7 | # rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# 8 | # rdfs: http://www.w3.org/2000/01/rdf-schema# 9 | # skos: http://www.w3.org/2004/02/skos/core# 10 | # sssom: https://w3id.org/sssom/ 11 | # orcid: https://orcid.org/ 12 | # obo: http://purl.obolibrary.org/obo/ 13 | # semapv: https://w3id.org/semapv/vocab/ 14 | # license: https://creativecommons.org/publicdomain/zero/1.0/ 15 | # mapping_provider: https://www.mousephenotype.org 16 | # mapping_set_description: 'The IMPC Mouse Morphology Mappings: Gross Pathology & Tissue 17 | # Collection Test (PATO)' 18 | # mapping_set_id: https://w3id.org/sssom/commons/mouse-human/mappings/pato_hp_pat_impc.sssom.tsv 19 | subject_id subject_label predicate_id object_id object_label mapping_justification 20 | PATO:0000317 black skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 21 | PATO:0000318 blue skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 22 | PATO:0000320 green skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 23 | PATO:0000322 red skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 24 | PATO:0000323 white skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 25 | PATO:0000324 yellow skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 26 | PATO:0000366 left skos:closeMatch HP:0012835 Left semapv:LexicalMatching 27 | PATO:0000367 right skos:closeMatch HP:0012834 Right semapv:LexicalMatching 28 | PATO:0000386 hard skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 29 | PATO:0000387 soft skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 30 | PATO:0000407 flat skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 31 | PATO:0000411 circular skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 32 | PATO:0000573 increased length skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 33 | PATO:0000574 decreased length skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 34 | PATO:0000586 increased size skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 35 | PATO:0000587 decreased size skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 36 | PATO:0000618 bilateral skos:closeMatch HP:0012832 Bilateral semapv:LexicalMatching 37 | PATO:0000627 focal skos:exactMatch HP:0030650 Focal semapv:LexicalMatching 38 | PATO:0000632 symmetrical skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 39 | PATO:0000634 unilateral skos:closeMatch HP:0012833 Unilateral semapv:LexicalMatching 40 | PATO:0000950 grey skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 41 | PATO:0000952 brown skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 42 | PATO:0000954 pink skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 43 | PATO:0001369 raised skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 44 | PATO:0001566 diffuse skos:closeMatch HP:0020034 Diffuse semapv:LexicalMatching 45 | PATO:0001791 multifocal (preferred synonym of multi-localised) skos:closeMatch HP:0030651 Multifocal semapv:LexicalMatching 46 | PATO:0001891 ovate skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 47 | PATO:0002274 mottled skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 48 | PATO:0002376 inflated skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 49 | PATO:0002401 random pattern skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 50 | PATO:0002402 multifocal to coalescing skos:closeMatch HP:0030651 Multifocal semapv:LogicalReasoning 51 | PATO:0002406 friable skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 52 | PATO:0002408 watery skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 53 | PATO:0002409 fluid-filled skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 54 | PATO:0002410 beige skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 55 | PATO:0002416 sunken skos:closeMatch sssom:NoTermFound semapv:ManualMappingCuration 56 | -------------------------------------------------------------------------------- /mhmi_analysis.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "markdown", 5 | "metadata": {}, 6 | "source": [ 7 | "# Mapping analysis for datasets in the Mouse-Human mapping effort\n", 8 | "\n", 9 | "More information can be found here: https://github.com/obophenotype/mp_hp_mapping" 10 | ] 11 | }, 12 | { 13 | "cell_type": "code", 14 | "execution_count": 69, 15 | "metadata": {}, 16 | "outputs": [ 17 | { 18 | "name": "stdout", 19 | "output_type": "stream", 20 | "text": [ 21 | "Last run: 2020-12-10 16:21:04.986420\n" 22 | ] 23 | } 24 | ], 25 | "source": [ 26 | "import datetime\n", 27 | "import pandas as pd\n", 28 | "import numpy as np\n", 29 | "import pathlib\n", 30 | "\n", 31 | "print(f\"Last run: {datetime.datetime.now()}\")" 32 | ] 33 | }, 34 | { 35 | "cell_type": "code", 36 | "execution_count": 46, 37 | "metadata": {}, 38 | "outputs": [], 39 | "source": [ 40 | "human_phenotype = \"human_phenotype\"\n", 41 | "mammalian_phenotype = \"mammalian_phenotype\"\n", 42 | "obo_iri_prefix = \"http://purl.obolibrary.org/obo/\"\n", 43 | "mp_iri_prefix = \"http://purl.obolibrary.org/obo/MP_\"\n", 44 | "hp_iri_prefix = \"http://purl.obolibrary.org/obo/HP_\"" 45 | ] 46 | }, 47 | { 48 | "cell_type": "code", 49 | "execution_count": 40, 50 | "metadata": {}, 51 | "outputs": [], 52 | "source": [ 53 | "use_case_dir = \"use_cases\"\n", 54 | "sources_dir = \"sources\"\n", 55 | "\n", 56 | "use_cases = {\n", 57 | " \"kids_first\": pathlib.Path.cwd().joinpath(use_case_dir, \"April2020_KF_Data_Phenotypes_HPO.csv\")\n", 58 | "}\n", 59 | "raw_mapping_data = {\n", 60 | " \"upheno_logical\": pathlib.Path.cwd().joinpath(sources_dir,\"upheno\", \"upheno_mapping_logical.csv\"),\n", 61 | " \"upheno_lexical\": pathlib.Path.cwd().joinpath(sources_dir,\"upheno\", \"upheno_mapping_lexical.csv\")\n", 62 | "}\n", 63 | " " 64 | ] 65 | }, 66 | { 67 | "cell_type": "markdown", 68 | "metadata": {}, 69 | "source": [ 70 | "# Load data\n", 71 | "## Load use case data\n", 72 | "### Load Kids First data" 73 | ] 74 | }, 75 | { 76 | "cell_type": "code", 77 | "execution_count": 41, 78 | "metadata": {}, 79 | "outputs": [ 80 | { 81 | "data": { 82 | "text/plain": [ 83 | "0 HP:0030319\n", 84 | "1 HP:0040106\n", 85 | "2 HP:0040064\n", 86 | "3 HP:0001252\n", 87 | "4 HP:0001999\n", 88 | " ... \n", 89 | "782 HP:0000807\n", 90 | "783 HP:0011805\n", 91 | "784 HP:0010741\n", 92 | "785 HP:0002992\n", 93 | "786 HP:0009736\n", 94 | "Name: human_phenotype, Length: 787, dtype: object" 95 | ] 96 | }, 97 | "execution_count": 41, 98 | "metadata": {}, 99 | "output_type": "execute_result" 100 | } 101 | ], 102 | "source": [ 103 | "df_kids_first = pd.read_csv(use_cases['kids_first'])\n", 104 | "df_kids_first[human_phenotype]=df_kids_first['hpo_id_phenotype']\n", 105 | "df_kids_first = df_kids_first[human_phenotype]\n", 106 | "df_kids_first" 107 | ] 108 | }, 109 | { 110 | "cell_type": "markdown", 111 | "metadata": {}, 112 | "source": [ 113 | "## Load mapping data\n", 114 | "### Load upheno mappings" 115 | ] 116 | }, 117 | { 118 | "cell_type": "code", 119 | "execution_count": 77, 120 | "metadata": {}, 121 | "outputs": [ 122 | { 123 | "name": "stdout", 124 | "output_type": "stream", 125 | "text": [ 126 | "929\n", 127 | "1711\n", 128 | " human_phenotype mammalian_phenotype\n", 129 | "2 HP:0012091 MP:0002693\n", 130 | "11 HP:0002208 MP:0002832\n", 131 | "21 HP:0003537 MP:0008822\n", 132 | "23 HP:0002558 MP:0009723\n", 133 | "29 HP:3000052 MP:0003056\n", 134 | " human_phenotype mammalian_phenotype\n", 135 | "0 HP:0000347 MP:0002639\n", 136 | "2 HP:0000347 MP:0004592\n", 137 | "5 HP:0000327 MP:0004540\n", 138 | "6 HP:0005736 MP:0002764\n", 139 | "9 HP:0003270 MP:0009247\n" 140 | ] 141 | } 142 | ], 143 | "source": [ 144 | "def extract_upheno_mappings(df_upheno):\n", 145 | " df_upheno = df_upheno[[\"p1\", \"p2\"]]\n", 146 | " df_upheno = df_upheno[(df_upheno.p1.str.startswith(hp_iri_prefix)) & (df_upheno.p2.str.startswith(mp_iri_prefix))]\n", 147 | " df_upheno[\"p1\"] = df_upheno.p1.str.replace(obo_iri_prefix,\"\")\n", 148 | " df_upheno[\"p1\"] = df_upheno.p1.str.replace(\"_\",\":\")\n", 149 | " df_upheno[\"p2\"] = df_upheno.p2.str.replace(\"_\",\":\")\n", 150 | " df_upheno[\"p2\"] = df_upheno.p2.str.replace(obo_iri_prefix,\"\")\n", 151 | " df_upheno.columns = [human_phenotype,mammalian_phenotype]\n", 152 | " return df_upheno\n", 153 | "\n", 154 | "dfm_upheno_logical = extract_upheno_mappings(pd.read_csv(raw_mapping_data['upheno_logical']))\n", 155 | "dfm_upheno_lexical = extract_upheno_mappings(pd.read_csv(raw_mapping_data['upheno_lexical']))\n", 156 | "print(len(dfm_upheno_logical))\n", 157 | "print(len(dfm_upheno_lexical))\n", 158 | "print(dfm_upheno_logical.head())\n", 159 | "print(dfm_upheno_lexical.head())" 160 | ] 161 | }, 162 | { 163 | "cell_type": "markdown", 164 | "metadata": {}, 165 | "source": [ 166 | "# Map data\n", 167 | "## Kids First" 168 | ] 169 | }, 170 | { 171 | "cell_type": "code", 172 | "execution_count": 78, 173 | "metadata": {}, 174 | "outputs": [ 175 | { 176 | "data": { 177 | "text/html": [ 178 | "
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human_phenotypemammalian_phenotypeupheno_logicalupheno_lexical
0HP:0030319NaNFalseFalse
1HP:0040106NaNFalseFalse
2HP:0040064NaNFalseFalse
3HP:0001252NaNFalseFalse
4HP:0001999MP:0003743TrueTrue
...............
782HP:0000807NaNFalseFalse
783HP:0011805NaNFalseFalse
784HP:0010741NaNFalseFalse
785HP:0002992MP:0000558TrueTrue
786HP:0009736NaNFalseFalse
\n", 282 | "

787 rows × 4 columns

\n", 283 | "
" 284 | ], 285 | "text/plain": [ 286 | " human_phenotype mammalian_phenotype upheno_logical upheno_lexical\n", 287 | "0 HP:0030319 NaN False False\n", 288 | "1 HP:0040106 NaN False False\n", 289 | "2 HP:0040064 NaN False False\n", 290 | "3 HP:0001252 NaN False False\n", 291 | "4 HP:0001999 MP:0003743 True True\n", 292 | ".. ... ... ... ...\n", 293 | "782 HP:0000807 NaN False False\n", 294 | "783 HP:0011805 NaN False False\n", 295 | "784 HP:0010741 NaN False False\n", 296 | "785 HP:0002992 MP:0000558 True True\n", 297 | "786 HP:0009736 NaN False False\n", 298 | "\n", 299 | "[787 rows x 4 columns]" 300 | ] 301 | }, 302 | "execution_count": 78, 303 | "metadata": {}, 304 | "output_type": "execute_result" 305 | } 306 | ], 307 | "source": [ 308 | "def merge_mappings(df,dfm,mapping=\"mapping\"):\n", 309 | " df = df.merge(dfm, how=\"left\")\n", 310 | " df[mapping] = ~df['mammalian_phenotype'].isna()\n", 311 | " return df\n", 312 | "\n", 313 | "df_kids_first_mapped = merge_mappings(df_kids_first.to_frame(), dfm_upheno_logical,\"upheno_logical\")\n", 314 | "df_kids_first_mapped = merge_mappings(df_kids_first_mapped, dfm_upheno_lexical,\"upheno_lexical\")\n", 315 | "df_kids_first_mapped.to_csv(\"df_kids_first_mapped.csv\")\n", 316 | "df_kids_first_mapped" 317 | ] 318 | }, 319 | { 320 | "cell_type": "code", 321 | "execution_count": 66, 322 | "metadata": {}, 323 | "outputs": [ 324 | { 325 | "data": { 326 | "text/plain": [ 327 | "False 663\n", 328 | "True 124\n", 329 | "Name: upheno_logical, dtype: int64" 330 | ] 331 | }, 332 | "execution_count": 66, 333 | "metadata": {}, 334 | "output_type": "execute_result" 335 | } 336 | ], 337 | "source": [ 338 | "df_kids_first_mapped.upheno_logical.value_counts()" 339 | ] 340 | }, 341 | { 342 | "cell_type": "code", 343 | "execution_count": 65, 344 | "metadata": {}, 345 | "outputs": [ 346 | { 347 | "data": { 348 | "text/plain": [ 349 | "False 663\n", 350 | "True 124\n", 351 | "Name: upheno_lexical, dtype: int64" 352 | ] 353 | }, 354 | "execution_count": 65, 355 | "metadata": {}, 356 | "output_type": "execute_result" 357 | } 358 | ], 359 | "source": [ 360 | "df_kids_first_mapped.upheno_lexical.value_counts()" 361 | ] 362 | }, 363 | { 364 | "cell_type": "code", 365 | "execution_count": 70, 366 | "metadata": {}, 367 | "outputs": [ 368 | { 369 | "data": { 370 | "text/html": [ 371 | "
\n", 372 | "\n", 385 | "\n", 386 | " \n", 387 | " \n", 388 | " \n", 389 | " \n", 390 | " \n", 391 | " \n", 392 | " \n", 393 | " \n", 394 | " \n", 395 | " \n", 396 | " \n", 397 | " \n", 398 | " \n", 399 | " \n", 400 | " \n", 401 | " \n", 402 | " \n", 403 | " \n", 404 | " \n", 405 | " \n", 406 | " \n", 407 | " \n", 408 | " \n", 409 | " \n", 410 | " \n", 411 | " \n", 412 | " \n", 413 | " \n", 414 | " \n", 415 | " \n", 416 | " \n", 417 | " \n", 418 | " \n", 419 | " \n", 420 | " \n", 421 | " \n", 422 | " \n", 423 | " \n", 424 | " \n", 425 | " \n", 426 | " \n", 427 | " \n", 428 | " \n", 429 | " \n", 430 | " \n", 431 | " \n", 432 | " \n", 433 | " \n", 434 | " \n", 435 | " \n", 436 | " \n", 437 | " \n", 438 | " \n", 439 | " \n", 440 | " \n", 441 | " \n", 442 | " \n", 443 | " \n", 444 | " \n", 445 | " \n", 446 | " \n", 447 | " \n", 448 | " \n", 449 | " \n", 450 | " \n", 451 | " \n", 452 | " \n", 453 | " \n", 454 | " \n", 455 | " \n", 456 | " \n", 457 | " \n", 458 | " \n", 459 | " \n", 460 | " \n", 461 | " \n", 462 | " \n", 463 | " \n", 464 | " \n", 465 | " \n", 466 | " \n", 467 | " \n", 468 | " \n", 469 | " \n", 470 | " \n", 471 | " \n", 472 | " \n", 473 | " \n", 474 | " \n", 475 | " \n", 476 | " \n", 477 | " \n", 478 | " \n", 479 | " \n", 480 | " \n", 481 | " \n", 482 | " \n", 483 | " \n", 484 | " \n", 485 | " \n", 486 | "
human_phenotypemammalian_phenotypeupheno_logicalupheno_lexicalcombined
0HP:0030319NaNFalseFalseFalse
1HP:0040106NaNFalseFalseFalse
2HP:0040064NaNFalseFalseFalse
3HP:0001252NaNFalseFalseFalse
4HP:0001999MP:0003743TrueTrueTrue
..................
782HP:0000807NaNFalseFalseFalse
783HP:0011805NaNFalseFalseFalse
784HP:0010741NaNFalseFalseFalse
785HP:0002992MP:0000558TrueTrueTrue
786HP:0009736NaNFalseFalseFalse
\n", 487 | "

787 rows × 5 columns

\n", 488 | "
" 489 | ], 490 | "text/plain": [ 491 | " human_phenotype mammalian_phenotype upheno_logical upheno_lexical \\\n", 492 | "0 HP:0030319 NaN False False \n", 493 | "1 HP:0040106 NaN False False \n", 494 | "2 HP:0040064 NaN False False \n", 495 | "3 HP:0001252 NaN False False \n", 496 | "4 HP:0001999 MP:0003743 True True \n", 497 | ".. ... ... ... ... \n", 498 | "782 HP:0000807 NaN False False \n", 499 | "783 HP:0011805 NaN False False \n", 500 | "784 HP:0010741 NaN False False \n", 501 | "785 HP:0002992 MP:0000558 True True \n", 502 | "786 HP:0009736 NaN False False \n", 503 | "\n", 504 | " combined \n", 505 | "0 False \n", 506 | "1 False \n", 507 | "2 False \n", 508 | "3 False \n", 509 | "4 True \n", 510 | ".. ... \n", 511 | "782 False \n", 512 | "783 False \n", 513 | "784 False \n", 514 | "785 True \n", 515 | "786 False \n", 516 | "\n", 517 | "[787 rows x 5 columns]" 518 | ] 519 | }, 520 | "execution_count": 70, 521 | "metadata": {}, 522 | "output_type": "execute_result" 523 | } 524 | ], 525 | "source": [ 526 | "df_kids_first_mapped['combined']=np.where( ( (df_kids_first_mapped.upheno_logical) | (df_kids_first_mapped.upheno_lexical)), True, False) \n", 527 | "df_kids_first_mapped" 528 | ] 529 | }, 530 | { 531 | "cell_type": "code", 532 | "execution_count": 72, 533 | "metadata": {}, 534 | "outputs": [ 535 | { 536 | "data": { 537 | "text/plain": [ 538 | "False 663\n", 539 | "True 124\n", 540 | "Name: combined, dtype: int64" 541 | ] 542 | }, 543 | "execution_count": 72, 544 | "metadata": {}, 545 | "output_type": "execute_result" 546 | } 547 | ], 548 | "source": [ 549 | "df_kids_first_mapped.combined.value_counts()" 550 | ] 551 | }, 552 | { 553 | "cell_type": "code", 554 | "execution_count": null, 555 | "metadata": {}, 556 | "outputs": [], 557 | "source": [] 558 | } 559 | ], 560 | "metadata": { 561 | "kernelspec": { 562 | "display_name": "Python 3", 563 | "language": "python", 564 | "name": "python3" 565 | }, 566 | "language_info": { 567 | "codemirror_mode": { 568 | "name": "ipython", 569 | "version": 3 570 | }, 571 | "file_extension": ".py", 572 | "mimetype": "text/x-python", 573 | "name": "python", 574 | "nbconvert_exporter": "python", 575 | "pygments_lexer": "ipython3", 576 | "version": "3.8.3" 577 | } 578 | }, 579 | "nbformat": 4, 580 | "nbformat_minor": 4 581 | } 582 | -------------------------------------------------------------------------------- /registry.yml: -------------------------------------------------------------------------------- 1 | mapping_registry_id: https://w3id.org/sssom/commons/mouse-human 2 | registry_title: Mouse Human Mapping Initiative 3 | registry_description: Mouse Human Mapping Initiative 4 | homepage: https://github.com/mapping-commons/mh_mapping_initiative 5 | documentation: https://github.com/mapping-commons/mh_mapping_initiative/blob/master/README.md 6 | mapping_set_references: 7 | - mapping_set_id: https://w3id.org/sssom/commons/mouse-human/mappings/mp_hp_eye_impc.sssom.tsv 8 | mapping_set_group: impc_mouse_morphology 9 | registry_confidence: 0.9 10 | local_name: mp_hp_eye_impc.sssom.tsv 11 | - mapping_set_id: https://w3id.org/sssom/commons/mouse-human/mappings/mp_hp_hwt_impc.sssom.tsv 12 | mapping_set_group: impc_mouse_morphology 13 | local_name: mp_hp_hwt_impc.sssom.tsv 14 | - mapping_set_id: https://w3id.org/sssom/commons/mouse-human/mappings/mp_hp_owt_impc.sssom.tsv 15 | mapping_set_group: impc_mouse_morphology 16 | local_name: mp_hp_owt_impc.sssom.tsv 17 | - mapping_set_id: https://w3id.org/sssom/commons/mouse-human/mappings/ma_uberon_pat_impc.sssom.tsv 18 | mapping_set_group: impc_mouse_morphology 19 | local_name: ma_uberon_pat_impc.sssom.tsv 20 | - mapping_set_id: https://w3id.org/sssom/commons/mouse-human/mappings/mp_hp_pat_impc.sssom.tsv 21 | mapping_set_group: impc_mouse_morphology 22 | local_name: mp_hp_pat_impc.sssom.tsv 23 | - mapping_set_id: https://w3id.org/sssom/commons/mouse-human/mappings/pato_hp_pat_impc.sssom.tsv 24 | mapping_set_group: impc_mouse_morphology 25 | local_name: pato_hp_pat_impc.sssom.tsv 26 | - mapping_set_id: https://w3id.org/sssom/commons/mouse-human/mappings/mp_hp_xry_impc.sssom.tsv 27 | mapping_set_group: impc_mouse_morphology 28 | local_name: mp_hp_xry_impc.sssom.tsv 29 | - mapping_set_id: https://w3id.org/sssom/commons/mouse-human/mappings/hp_doid_pistoia.sssom.tsv 30 | mapping_set_group: pistoia_mappings 31 | local_name: hp_doid_pistoia.sssom.tsv 32 | - mapping_set_id: https://w3id.org/sssom/commons/mouse-human/mappings/mp_doid_pistoia.sssom.tsv 33 | mapping_set_group: pistoia_mappings 34 | registry_confidence: 0.4 35 | local_name: mp_doid_pistoia.sssom.tsv 36 | - mapping_set_id: https://w3id.org/sssom/commons/mouse-human/mappings/mp_hp_pistoia.sssom.tsv 37 | mapping_set_group: pistoia_mappings 38 | local_name: mp_hp_pistoia.sssom.tsv 39 | - mapping_set_id: https://w3id.org/sssom/commons/mouse-human/mappings/ordo_doid_pistoia.sssom.tsv 40 | mapping_set_group: pistoia_mappings 41 | local_name: ordo_doid_pistoia.sssom.tsv 42 | - mapping_set_id: https://w3id.org/sssom/commons/mouse-human/mappings/ordo_mp_pistoia.sssom.tsv 43 | mapping_set_group: pistoia_mappings 44 | local_name: ordo_mp_pistoia.sssom.tsv 45 | - mapping_set_id: https://w3id.org/sssom/commons/mouse-human/mappings/mp_hp_mgi_all.sssom.tsv 46 | mapping_set_group: mgi_mappings 47 | local_name: mp_hp_mgi_all.sssom.tsv 48 | -------------------------------------------------------------------------------- /scripts/lib.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python3 2 | 3 | import yaml 4 | import logging 5 | import subprocess 6 | import threading 7 | import urllib.request 8 | import hashlib 9 | from subprocess import check_call 10 | import requests 11 | from datetime import datetime 12 | 13 | obo_purl = "http://purl.obolibrary.org/obo/" 14 | 15 | class Command(object): 16 | def __init__(self, cmd): 17 | self.cmd = cmd 18 | self.process = None 19 | 20 | def run(self, timeout): 21 | def target(): 22 | logging.info(f"RUNNING: {self.cmd} (Timeout: {timeout})") 23 | self.process = subprocess.Popen(self.cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True) 24 | (out, err) = self.process.communicate() 25 | logging.info('OUT: {}'.format(out)) 26 | if err: 27 | logging.info('ERROR: {}'.format(err)) 28 | 29 | thread = threading.Thread(target=target) 30 | thread.start() 31 | 32 | thread.join(timeout) 33 | if thread.is_alive(): 34 | print('Terminating process') 35 | self.process.terminate() 36 | thread.join() 37 | if self.process.returncode != 0: 38 | raise Exception(f'Failed: {self.cmd} with return code {self.process.returncode}') 39 | 40 | 41 | def runcmd(cmd, timeout=3600): 42 | command = Command(cmd) 43 | command.run(timeout=timeout) 44 | 45 | 46 | def read_txt_from_url_as_lines(url): 47 | profile_raw = urllib.request.urlopen(url).read() 48 | profile_lines = profile_raw.decode('utf-8').split('\n') 49 | return profile_lines 50 | 51 | 52 | def open_yaml_from_url(url): 53 | raw = urllib.request.urlopen(url).read() 54 | return yaml.load(raw, Loader=yaml.SafeLoader) 55 | 56 | 57 | class RegistryFile: 58 | 59 | def __init__(self, config_file): 60 | self.config = yaml.load(open(config_file, 'r'), Loader=yaml.SafeLoader) 61 | 62 | def get_registry_id(self): 63 | if "registry_id" in self.config: 64 | return self.config.get("registry_id") 65 | else: 66 | return "unknown" 67 | 68 | def get_mapping_dir(self): 69 | if "mapping_dir" in self.config: 70 | return self.config.get("mapping_dir") 71 | else: 72 | return "mappings" 73 | 74 | def get_registry_title(self): 75 | if "registry_title" in self.config: 76 | return self.config.get("registry_title") 77 | else: 78 | return "unknown" 79 | 80 | def get_registry_description(self): 81 | if "registry_description" in self.config: 82 | return self.config.get("registry_description") 83 | else: 84 | return "No description provided." 85 | 86 | 87 | def get_mapping_ids(self): 88 | mapping_ids = [] 89 | mappings = self.config.get("mappings") 90 | 91 | for o in mappings: 92 | mapping_ids.append(o['mapping_set_id']) 93 | return list(set(mapping_ids)) 94 | 95 | def get_mappings(self): 96 | mappings = self.config.get("mappings") 97 | mappings_indexed = {} 98 | 99 | for m in mappings: 100 | mappings_indexed[m['mapping_set_id']]=m 101 | 102 | return mappings_indexed 103 | 104 | 105 | def is_number(s): 106 | try: 107 | float(s) 108 | return True 109 | except ValueError: 110 | return False 111 | 112 | def sha256sum(filename): 113 | h = hashlib.sha256() 114 | b = bytearray(128*1024) 115 | mv = memoryview(b) 116 | with open(filename, 'rb', buffering=0) as f: 117 | for n in iter(lambda : f.readinto(mv), 0): 118 | h.update(mv[:n]) 119 | return h.hexdigest() 120 | 121 | def load_yaml(filepath): 122 | with open(filepath, 'r') as f: 123 | data = yaml.load(f, Loader=yaml.SafeLoader) 124 | return data 125 | 126 | 127 | def robot_prepare_ontology(o_path, o_out_path, o_metrics_path, base_iris, make_base, robot_prefixes={}, robot_opts="-v"): 128 | logging.info(f"Preparing {o_path} for dashboard.") 129 | try: 130 | callstring = ['robot','measure'] 131 | if robot_opts: 132 | callstring.append(f"{robot_opts}") 133 | callstring.extend(['-i', o_path]) 134 | for prefix in robot_prefixes: 135 | callstring.extend(['--prefix', f"{prefix}: {robot_prefixes[prefix]}"]) 136 | callstring.extend(['--metrics', 'extended-reasoner','-f','yaml','-o',o_metrics_path, 'merge']) 137 | if make_base: 138 | callstring.extend(['remove']) 139 | #base_iris_string = " ".join([f"--base-iri \"{s}\"" for s in sbase_iris]) 140 | for s in base_iris: 141 | callstring.extend(['--base-iri',s]) 142 | callstring.extend(["--axioms", "external", "-p", "false"]) 143 | callstring.extend(['--output', o_out_path]) 144 | logging.info(callstring) 145 | check_call(callstring) 146 | except Exception as e: 147 | raise Exception(f"Preparing {o_path} for dashboard failed...", e) 148 | 149 | def count_up(dictionary, value): 150 | if value not in dictionary: 151 | dictionary[value] = 0 152 | dictionary[value] = dictionary[value] + 1 153 | return dictionary 154 | 155 | 156 | def save_yaml(dictionary, file_path): 157 | with open(file_path, 'w') as file: 158 | yaml.dump(dictionary, file) 159 | 160 | 161 | 162 | def get_hours_since(timestamp): 163 | modified_date = datetime.fromtimestamp(timestamp) 164 | now = datetime.now() 165 | duration = now - modified_date 166 | hours_since = (duration.total_seconds() // 3600) 167 | return hours_since 168 | 169 | def compute_obo_score(impact, reuse, dashboard, impact_external, weights): 170 | impact_weight = weights['impact'] 171 | reuse_weight = weights['reuse'] 172 | dashboard_weight = weights['dashboard'] 173 | impact_external_weight = weights['impact_external'] 174 | #sum_weights = impact_weight + reuse_weight + dashboard_weight + impact_external_weight 175 | #score_sum = sum([impact_weight * impact, reuse_weight * reuse, dashboard_weight * dashboard, 176 | # impact_external_weight * impact_external]) 177 | #formula = f"({impact_weight}*impact+{dashboard_weight}*dashboard+{reuse_weight}*reuse+{impact_external_weight}*impact_external)/{sum_weights}" 178 | 179 | sum_weights = impact_weight+dashboard_weight 180 | score_sum = sum([impact_weight*impact, dashboard_weight*dashboard]) 181 | formula = f"({impact_weight}*impact+{dashboard_weight}*dashboard)/{sum_weights}" 182 | score = score_sum/sum_weights 183 | return { "score": score, "formula" : formula } 184 | 185 | 186 | def compute_dashboard_score(data, weights, maximpacts): 187 | 188 | if 'failure' in data: 189 | return 0 190 | 191 | oboscore = 100 192 | no_base = 0 193 | report_errors = 0 194 | report_warning = 0 195 | report_info = 0 196 | 197 | overall_error = 0 198 | overall_warning = 0 199 | overall_info = 0 200 | 201 | if 'base_generated' in data and data['base_generated'] == True: 202 | no_base = weights['no_base'] 203 | 204 | if 'results' in data: 205 | if 'ROBOT Report' in data['results']: 206 | if 'results' in data['results']['ROBOT Report']: 207 | report_errors = data['results']['ROBOT Report']['results']['ERROR'] 208 | report_warning = data['results']['ROBOT Report']['results']['WARN'] 209 | report_info = data['results']['ROBOT Report']['results']['INFO'] 210 | 211 | if 'summary' in data: 212 | overall_error = data['summary']['summary_count']['ERROR'] 213 | overall_warning = data['summary']['summary_count']['WARN'] 214 | overall_info = data['summary']['summary_count']['INFO'] 215 | 216 | oboscore = oboscore - score_max(weights['no_base'] * no_base, maximpacts['no_base']) 217 | oboscore = oboscore - score_max(weights['overall_error'] * overall_error, maximpacts['overall_error']) 218 | oboscore = oboscore - score_max(weights['overall_warning'] * overall_warning, maximpacts['overall_warning']) 219 | oboscore = oboscore - score_max(weights['overall_info'] * overall_info, maximpacts['overall_info']) 220 | oboscore = oboscore - score_max(weights['report_errors'] * report_errors, maximpacts['report_errors']) 221 | oboscore = oboscore - score_max(weights['report_warning'] * report_warning, maximpacts['report_warning']) 222 | oboscore = oboscore - score_max(weights['report_info'] * report_info, maximpacts['report_info']) 223 | return "%.2f" % oboscore 224 | 225 | 226 | def round_float(n): 227 | strfloat = "%.3f" % n 228 | return (float(strfloat)) 229 | 230 | def score_max(score,maxscore): 231 | if score > maxscore: 232 | return maxscore 233 | else: 234 | return score 235 | 236 | def get_prefix_from_url_namespace(ns, curie_map): 237 | for prefix in curie_map: 238 | if ns==curie_map[prefix]: 239 | return prefix 240 | if ns.startswith(obo_purl) and ns.endswith("_"): 241 | ns = ns.replace(obo_purl,"") 242 | ns = ns[:-1] 243 | return ns 244 | msg = f"Namespace {ns} not found in curie map, aborting.." 245 | raise Exception(msg) 246 | 247 | def get_base_prefixes(curie_map, base_namespaces): 248 | internal_ns = [] 249 | for ns in base_namespaces: 250 | prefix = get_prefix_from_url_namespace(ns, curie_map) 251 | internal_ns.append(prefix) 252 | return internal_ns 253 | 254 | def compute_percentage_reused_entities(entity_use_map, internal_ns): 255 | internal_entities = 0 256 | external_entities = 0 257 | for prefix in entity_use_map: 258 | if prefix in internal_ns: 259 | internal_entities += entity_use_map[prefix] 260 | else: 261 | external_entities += entity_use_map[prefix] 262 | 263 | reuse_score = 100*(external_entities/(external_entities+internal_entities)) 264 | score_string = "%.2f" % round(reuse_score, 2) 265 | return float(score_string) 266 | -------------------------------------------------------------------------------- /scripts/update_registry.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python3 2 | 3 | import os 4 | import yaml 5 | import click 6 | import logging 7 | 8 | from lib import RegistryFile, runcmd, save_yaml 9 | 10 | logging.basicConfig(level=logging.INFO) 11 | 12 | @click.group() 13 | def cli(): 14 | pass 15 | 16 | 17 | @cli.command() 18 | @click.option('-r', '--registryfile', type=click.Path(exists=True), 19 | help=""" 20 | path to a YAML registry file. 21 | """) 22 | def update_registry(registryfile): 23 | config = RegistryFile(registryfile) 24 | make_parameters=" -B" 25 | mapping_dir = config.get_mapping_dir() 26 | 27 | if not os.path.isdir(mapping_dir): 28 | os.mkdir(mapping_dir) 29 | 30 | mappings = config.get_mappings() 31 | 32 | for mapping in mappings: 33 | mappings_set_file_path_tsv = os.path.join(mapping_dir, f"{mapping}.sssom.tsv") 34 | logging.info(f"Updateing {mapping} mapping set") 35 | runcmd(f"make mappings/{mapping}.sssom.tsv {make_parameters}") 36 | 37 | if __name__ == '__main__': 38 | cli() 39 | -------------------------------------------------------------------------------- /sources/README.md: -------------------------------------------------------------------------------- 1 | # Mouse-human mapping sources 2 | 3 | - [The IMPC Mouse Morphology Mappings](#the-impc-mouse-morphology-mappings) 4 | - [The MMHCdb Mappings](#the-MMHCdb-mappings) 5 | - [The UBERON Mappings](#the-uberon-mappings) 6 | - [The uPheno Mappings](#the-upheno-mappings) 7 | - [The Pistoia Alliance Mappings](#the-pistoia-alliance-mappings) 8 | 9 | ### The IMPC Mouse Morphology Mappings 10 | _Full name_: IMPC mouse morphology test terms and definitions mapped to HP and Uberon 11 | 12 | _Contact_: [Colin McKerlie](https://orcid.org/0000-0002-2232-0967) 13 | 14 | _Summary_: The current version of the International Mouse Phenotyping Consortium’s (IMPC) Morphology tests ontologies with manual mapping to HP and UBERON. 15 | 16 | _Raw data_: [download](impc) 17 | 18 | _Description_: The IMPC's vision is to be a provider of a comprehensive data and biological resource of in vivo mammalian gene function and dysfunction to inform human health and disease. IMPC phenotyping Centres around the world use a standardized mouse phenotyping pipeline of sequential tests to identify the function of uncharacterized genes and the pleiotropic consequences of gene dysfunction. Each of these tests requires and uses a common vocabulary of coded terms and definitions to describe test results. The IMPC’s Morphology Test Workgroup developed this set of coded terms and definitions by curating from existing ‘gold-standard’ mouse research ontologies; the Mouse Adult Gross Anatomy Ontology, the Mammalian Phenotype Ontology, and the Phenotype and Trait Ontology. The challenge now is to determine how translatable this set of coded terms and definitions that describe abnormalities in mice is to abnormal phenotypes in humans. 19 | 20 | - [Eye Morphology Test (uses MP)](https://www.mousephenotype.org/impress/ProcedureInfo?action=list&procID=924&pipeID=7): `IMPC_EYE_003 MP terms 30 Oct 2020.xlsx` 21 | - [X-ray Test (uses MP)](https://www.mousephenotype.org/impress/ProcedureInfo?action=list&procID=556&pipeID=7): `IMPC_XRY_003 MP terms 30 Oct 2020.xlsx` 22 | - [Heart Weight Test (uses MP)](https://www.mousephenotype.org/impress/ProcedureInfo?action=list&procID=601&pipeID=7): `IMPC_HWT_003 MP terms 30 Oct 2020.xlsx` 23 | - [Organ Weight Test (uses MP)](https://www.mousephenotype.org/impress/ProcedureInfo?action=list&procID=939&pipeID=7): `IMPC_OWT_003 MP terms 30 Oct 2020.xlsx` 24 | - [Gross Pathology & Tissue Collection Test (uses MA, MP, PATO)](https://www.mousephenotype.org/impress/ProcedureInfo?action=list&procID=775&pipeID=7): 25 | - `IMPC_PAT_003 MA terms 30 Oct 2020.xlsx` 26 | - `IMPC_PAT_003 MP terms 30 Oct 2020.xlsx` 27 | - `IMPC_PAT_003 PATO terms 30 Oct 2020.xlsx` 28 | 29 | _License_: All of the content, in its entirety, is a public resource so posting into a public repository or using the content for any appropriate use is permitted. 30 | 31 | ### The MMHCdb Mappings 32 | - [MMHCDB-NCIT-DO-NCIT](sources/mmhcdb/) 33 | - [MMHCD Vocabulary](sources/mmhcdb/) 34 | 35 | The MMHCdb Mappings are primarily concerned with mapping (mouse) tumors to Human ones (NCIT, DO). 36 | _Contact:_ [Debbie Krupke (JAX)](https://www.jax.org/people/debbie-krupke) 37 | 38 | ### The Uberon Mappings 39 | 40 | ### The uPheno Mappings 41 | 42 | #### Manually curated XREFs 43 | 44 | #### Lexical matches (Monarch) 45 | 46 | #### Logical matches (Monarch/Alliance) 47 | 48 | ### The Pistoia Alliance Mappings 49 | _Contact_: [Thomas Liener](https://github.com/LLTommy) 50 | _Summary_: The Pistoia alliance mappings use a mixture of label matching and ontology cross-links to automatically produce ontology alignments, using a system called PAXO. 51 | _Project_URL_: https://www.pistoiaalliance.org/projects/current-projects/ontologies-mapping/ 52 | _Raw data_: [snapshot](pistoia) 53 | _Description_: Data was cut off at a confidence of 0.9 after manual sanity checks. The data referenced here corresponds to a 2018 snapshot of the PAXO mapping pipeline. Datafiles available: 54 | - calculated_output_hp_doid.csv 55 | - calculated_output_mp_doid.csv 56 | - calculated_output_mp_hp.csv 57 | - calculated_output_ordo_doid.csv 58 | - calculated_output_ordo_hp.csv 59 | - calculated_output_ordo_mp.csv 60 | 61 | 62 | ### The MGI mappings 63 | - [MP-EMAPA](http://www.informatics.jax.org/downloads/reports/MP_EMAPA.rpt). 64 | 65 | _Contact:_ [Terry Hayamizu](https://www.jax.org/research-and-faculty/research-labs/the-ringwald-lab#) 66 | 67 | # Ontologies 68 | 69 | - MP-HP 70 | - MA-UBERON 71 | - MPATH-DO 72 | - MPATH-NCIT 73 | - 74 | -------------------------------------------------------------------------------- /sources/impc/IMPC_EYE_003 MP terms 30 Oct 2020.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mapping-commons/mh_mapping_initiative/ad95b5e6eec7ba0c744c32a684aa22407a324210/sources/impc/IMPC_EYE_003 MP terms 30 Oct 2020.xlsx -------------------------------------------------------------------------------- /sources/impc/IMPC_HWT_003 MP terms 30 Oct 2020.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mapping-commons/mh_mapping_initiative/ad95b5e6eec7ba0c744c32a684aa22407a324210/sources/impc/IMPC_HWT_003 MP terms 30 Oct 2020.xlsx -------------------------------------------------------------------------------- /sources/impc/IMPC_OWT_003 MP terms 30 Oct 2020.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mapping-commons/mh_mapping_initiative/ad95b5e6eec7ba0c744c32a684aa22407a324210/sources/impc/IMPC_OWT_003 MP terms 30 Oct 2020.xlsx -------------------------------------------------------------------------------- /sources/impc/IMPC_PAT_003 MA terms 30 Oct 2020.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mapping-commons/mh_mapping_initiative/ad95b5e6eec7ba0c744c32a684aa22407a324210/sources/impc/IMPC_PAT_003 MA terms 30 Oct 2020.xlsx -------------------------------------------------------------------------------- /sources/impc/IMPC_PAT_003 MP terms 30 Oct 2020.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mapping-commons/mh_mapping_initiative/ad95b5e6eec7ba0c744c32a684aa22407a324210/sources/impc/IMPC_PAT_003 MP terms 30 Oct 2020.xlsx -------------------------------------------------------------------------------- /sources/impc/IMPC_PAT_003 PATO terms 30 Oct 2020.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mapping-commons/mh_mapping_initiative/ad95b5e6eec7ba0c744c32a684aa22407a324210/sources/impc/IMPC_PAT_003 PATO terms 30 Oct 2020.xlsx -------------------------------------------------------------------------------- /sources/impc/IMPC_XRY_003 MP terms 30 Oct 2020.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mapping-commons/mh_mapping_initiative/ad95b5e6eec7ba0c744c32a684aa22407a324210/sources/impc/IMPC_XRY_003 MP terms 30 Oct 2020.xlsx -------------------------------------------------------------------------------- /sources/impc/README.md: -------------------------------------------------------------------------------- 1 | # IMPC mappings 2 | 3 | ## IMPC mapping methodology 4 | 5 | 1. Identify terms ... TODO 6 | 7 | ## Methodology to turn into SSSOM 8 | 9 | 1. From the raw mapping tables (xlsx format), we extract four column: 10 | 1. MP/MA/PATO ontology term 11 | 1. MP/MA/PATO ontology term name 12 | 1. HP/UBERON ontology term 13 | 1. HP/UBERON ontology term name 14 | 1. Given the official IMPC colour coding (Exact match: white; Lexical match: green; Logical match: yellow; No match: orange) the following default determinations are made: 15 | 1. `Exact match`: 16 | - match_type: SSSOM:Lexical 17 | - predicate_id: skos:exactMatch 18 | 1. `Lexical match`: 19 | - match_type: SSSOM:Lexical 20 | - predicate_id: skos:closeMatch 21 | 1. `Logical match`: 22 | - match_type: SSSOM:Logical 23 | - predicate_id: skos:closeMatch 24 | 1. `No match`: 25 | - match_type: SSSOM:HumanCurated 26 | - predicate_id: skos:closeMatch 27 | 1. After this default assignment, we asked two Mouse and two Human curators to review the resulting matches, and specify them if possible to one of the following: 28 | - skos:exactMatch 29 | - skos:narrowMatch 30 | - skos:broadMatch 31 | 32 | UPDATE 14 AUGUST 2022: 33 | 34 | We manually updated the mappings to use the correct format. -------------------------------------------------------------------------------- /sources/impc/basic_sssom_metadata.yml: -------------------------------------------------------------------------------- 1 | curie_map: 2 | HP: http://purl.obolibrary.org/obo/HP_ 3 | MP: http://purl.obolibrary.org/obo/MP_ 4 | PATO: http://purl.obolibrary.org/obo/PATO_ 5 | MA: http://purl.obolibrary.org/obo/MA_ 6 | UBERON: http://purl.obolibrary.org/obo/UBERON_ 7 | skos: http://www.w3.org/2004/02/skos/core# 8 | orcid: https://orcid.org/ 9 | ror: https://ror.org/ 10 | wikidata: https://www.wikidata.org/wiki/ 11 | obo: http://purl.obolibrary.org/obo/ 12 | semapv: https://w3id.org/semapv/ 13 | license: https://creativecommons.org/publicdomain/zero/1.0/ 14 | creator_id: orcid:0000-0002-2232-0967 15 | mapping_provider: https://www.mousephenotype.org 16 | -------------------------------------------------------------------------------- /sources/impc/sssom/impc_eye_003_mp_terms_30_oct_2020.tsv: -------------------------------------------------------------------------------- 1 | subject_id subject_label object_id object_label predicate_id mapping_justification reviewer_id 2 | MP:0001293 anophthalmia HP:0000528 Anophthalmia skos:exactMatch semapv:LexicalMatching orcid:0000-0002-7356-1779 3 | MP:0002750 exophthalmos HP:0000520 Proptosis skos:closeMatch semapv:LogicalReasoning 4 | MP:0006203 eye hemorrhage HP:0011885 Hemorrhage of the eye skos:exactMatch semapv:LexicalMatching orcid:0000-0002-7356-1779 5 | MP:0001340 abnormal eyelid morphology HP:0000492 Abnormal eyelid morphology skos:exactMatch semapv:LexicalMatching 6 | MP:0005176 eyelids fail to open HP:0009755 Ankyloblepharon skos:closeMatch semapv:LogicalReasoning 7 | MP:0005287 narrow eye opening HP:0045025 Narrow palpebral fissure skos:closeMatch semapv:LogicalReasoning 8 | MP:0001349 excessive tearing HP:0009926 Epiphora skos:closeMatch semapv:LogicalReasoning 9 | MP:0001312 abnormal cornea morphology HP:0000481 Abnormal cornea morphology skos:exactMatch semapv:LexicalMatching 10 | MP:0001314 corneal opacity HP:0007957 Corneal opacity skos:exactMatch semapv:LexicalMatching 11 | MP:0005542 corneal vascularization HP:0011496 Corneal neovascularization skos:closeMatch semapv:LexicalMatching 12 | MP:0012121 sclerocornea HP:0000647 Sclerocornea skos:exactMatch semapv:LexicalMatching 13 | MP:0009825 cornea ulcer HP:0012804 Corneal ulceration skos:closeMatch semapv:LexicalMatching 14 | MP:0005544 corneal deposits HP:0000531 Corneal crystals skos:closeMatch semapv:LogicalReasoning 15 | MP:0011962 increased cornea thickness HP:0011487 Increased corneal thickness skos:exactMatch semapv:LexicalMatching 16 | MP:0005543 decreased cornea thickness HP:0100689 Decreased corneal thickness skos:exactMatch semapv:LexicalMatching 17 | MP:0011962 increased cornea thickness HP:0011487 Increased corneal thickness skos:exactMatch semapv:LexicalMatching 18 | MP:0006241 abnormal placement of pupils HP:0009918 Ectopia pupillae skos:closeMatch semapv:LogicalReasoning 19 | MP:0006241 constricted or contracted pupil HP:0025309 Abnormal pupil shape skos:closeMatch semapv:LogicalReasoning 20 | MP:0001319 irregularly shaped pupil HP:0025309 Abnormal pupil shape skos:exactMatch semapv:LogicalReasoning 21 | MP:0002546 mydriasis HP:0011499 Mydriasis skos:exactMatch semapv:LexicalMatching 22 | MP:0002638 abnormal pupillary reflex HP:0007695 Abnormal pupillary light reflex skos:closeMatch semapv:LexicalMatching 23 | MP:0004222 iris synechia HP:0011483 Anterior synechiae of the anterior chamber skos:closeMatch semapv:LexicalMatching 24 | MP:0004222 iris synechia HP:0011484 Posterior synechiae of the anterior chamber skos:closeMatch semapv:LexicalMatching 25 | MP:0005102 abnormal iris pigmentation HP:0008034 Abnormal iris pigmentation skos:exactMatch semapv:LexicalMatching 26 | MP:0012122 abnormal iris transillumination HP:0012805 Iris transillumination defect skos:closeMatch semapv:LogicalReasoning 27 | MP:0001303 abnormal lens morphology HP:0000517 Abnormality of the lens skos:closeMatch semapv:LexicalMatching 28 | MP:0001304 cataract HP:0000518 Cataract skos:exactMatch semapv:LexicalMatching 29 | MP:0001307 fused cornea and lens HP:0011485 Corneolenticular adhesion skos:closeMatch semapv:LogicalReasoning 30 | MP:0008259 abnormal optic disc morphology HP:0012795 Abnormality of the optic disc skos:closeMatch semapv:LexicalMatching 31 | MP:0002792 abnormal retinal vasculature morphology HP:0008046 Abnormal retinal vascular morphology skos:closeMatch semapv:LexicalMatching 32 | MP:0010097 abnormal retinal blood vessel morphology HP:0008046 Abnormal retinal vascular morphology skos:closeMatch semapv:LexicalMatching 33 | MP:0010097 abnormal retinal blood vessel morphology HP:0008046 Abnormal retinal vascular morphology skos:closeMatch semapv:LexicalMatching 34 | MP:0011964 increased total retina thickness HP:0000479 Abnormal retinal morphology skos:closeMatch semapv:LogicalReasoning 35 | MP:0011965 decreased total retina thickness HP:0030329 Retinal thinning skos:closeMatch semapv:LogicalReasoning 36 | MP:0003733 abnormal retinal inner nuclear layer morphology HP:0000479 Abnormal retinal morphology skos:closeMatch semapv:LogicalReasoning 37 | MP:0003731 abnormal retinal outer nuclear layer morphology HP:0000479 Abnormal retinal morphology skos:closeMatch semapv:LogicalReasoning 38 | MP:0011964 increased total retina thickness HP:0000479 Abnormal retinal morphology skos:closeMatch semapv:LogicalReasoning 39 | MP:0011965 decreased total retina thickness HP:0030329 Retinal thinning skos:closeMatch semapv:LogicalReasoning 40 | MP:0003733 abnormal retinal inner nuclear layer morphology HP:0000479 Abnormal retinal morphology skos:closeMatch semapv:LogicalReasoning 41 | MP:0003731 abnormal retinal outer nuclear layer morphology HP:0000479 Abnormal retinal morphology skos:closeMatch semapv:LogicalReasoning 42 | MP:0001289 persistence of hyaloid vascular system HP:0007968 Remnants of the hyaloid vascular system skos:closeMatch semapv:LexicalMatching 43 | MP:0001325 abnormal retina morphology HP:0000479 Abnormal retinal morphology skos:closeMatch semapv:LexicalMatching 44 | MP:0011960 abnormal eye anterior chamber depth HP:0000593 Abnormal anterior chamber morphology skos:closeMatch semapv:LogicalReasoning 45 | MP:0011959 abnormal eye posterior chamber depth HP:0004329 Abnormal posterior eye segment morphology skos:closeMatch semapv:LogicalReasoning 46 | MP:0011960 abnormal eye anterior chamber depth HP:0000593 Abnormal anterior chamber morphology skos:closeMatch semapv:LogicalReasoning 47 | MP:0011959 abnormal eye posterior chamber depth HP:0004329 Abnormal posterior eye segment morphology skos:closeMatch semapv:LogicalReasoning 48 | MP:0002699 abnormal vitreous body morphology HP:0004327 Abnormal vitreous humor morphology skos:closeMatch semapv:LogicalReasoning 49 | -------------------------------------------------------------------------------- /sources/impc/sssom/impc_hwt_003_mp_terms_30_oct_2020.tsv: -------------------------------------------------------------------------------- 1 | subject_id subject_label object_id object_label mapping_justification predicate_id 2 | MP:0004357 long tibia HP:0010504 Increased length of the tibia semapv:LexicalMatching skos:closeMatch 3 | MP:0002764 short tibia HP:0005736 Short tibia semapv:LexicalMatching skos:closeMatch 4 | MP:0000558 abnormal tibia morphology HP:0002992 Abnormality of tibia morphology semapv:LexicalMatching skos:closeMatch 5 | MP:0001260 increased body weight HP:0004324 Increased body weight semapv:LexicalMatching skos:closeMatch 6 | MP:0001262 decreased body weight HP:0004325 Decreased body weight semapv:LexicalMatching skos:closeMatch 7 | MP:0001259 abnormal body weight HP:0004323 Abnormality of body weight semapv:LexicalMatching skos:closeMatch 8 | -------------------------------------------------------------------------------- /sources/impc/sssom/impc_owt_003_mp_terms_30_oct_2020.tsv: -------------------------------------------------------------------------------- 1 | subject_id subject_label object_id object_label mapping_justification predicate_id reviewer_id 2 | MP:0001260 increased body weight HP:0004324 Increased body weight semapv:LexicalMatching skos:exactMatch orcid:0000-0002-7356-1779 3 | MP:0001262 decreased body weight HP:0004325 Decreased body weight semapv:LexicalMatching skos:exactMatch orcid:0000-0002-7356-1779 4 | MP:0001259 abnormal body weight HP:0004323 Abnormality of body weight semapv:LexicalMatching skos:exactMatch orcid:0000-0002-7356-1779 5 | MP:0004952 increased spleen weight sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 6 | MP:0004953 decreased spleen weight sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 7 | MP:0004951 abnormal spleen weight HP:0001743 Abnormality of the spleen semapv:LogicalReasoning skos:narrowMatch orcid:0000-0002-7356-1779 8 | MP:0003917 increased kidney weight sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 9 | MP:0003918 decreased kidney weight sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 10 | MP:0002707 abnormal kidney weight HP:0000077 Abnormality of the kidney semapv:LogicalReasoning skos:closeMatch 11 | MP:0003917 increased kidney weight sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 12 | MP:0003918 decreased kidney weight sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 13 | MP:0002707 abnormal kidney weight HP:0000077 Abnormality of the kidney semapv:LogicalReasoning skos:closeMatch 14 | MP:0004928 increased epididymis weight sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 15 | MP:0004929 decreased epididymis weight sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 16 | MP:0004927 abnormal epididymis weight HP:0009714 Abnormality of the epididymis semapv:LogicalReasoning skos:closeMatch 17 | MP:0004909 increased seminal vesicle weight sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 18 | MP:0004910 decreased seminal vesicle weight sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 19 | MP:0004908 abnormal seminal vesicle weight sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 20 | MP:0004851 increased testis weight sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 21 | MP:0004852 decreased testis weight sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 22 | MP:0004850 abnormal testis weight HP:0000035 Abnormal testis morphology semapv:LogicalReasoning skos:closeMatch 23 | MP:0004851 increased testis weight sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 24 | MP:0004852 decreased testis weight sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 25 | MP:0004850 abnormal testis weight HP:0000035 Abnormal testis morphology semapv:LogicalReasoning skos:closeMatch 26 | MP:0002981 increased liver weight sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 27 | MP:0003402 decreased liver weight sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 28 | MP:0004847 abnormal liver weight HP:0001392 Abnormality of the liver semapv:LogicalReasoning skos:closeMatch 29 | MP:0005630 increased lung weight sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 30 | MP:0005631 decreased lung weight sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 31 | MP:0005629 abnormal lung weight HP:0002088 Abnormal lung morphology semapv:LogicalReasoning skos:closeMatch 32 | MP:0005630 increased lung weight sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 33 | MP:0005631 decreased lung weight sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 34 | MP:0005629 abnormal lung weight HP:0002088 Abnormal lung morphology semapv:LogicalReasoning skos:closeMatch 35 | -------------------------------------------------------------------------------- /sources/impc/sssom/impc_pat_003_ma_terms_30_oct_2020.tsv: -------------------------------------------------------------------------------- 1 | subject_id subject_label object_id object_label mapping_justification predicate_id 2 | MA:0000168 brain UBERON:0000955 brain semapv:LexicalMatching skos:exactMatch 3 | MA:0000261 eye UBERON:0000970 eye semapv:LexicalMatching skos:exactMatch 4 | MA:0001097 optic II nerve UBERON:0000941 cranial nerve II semapv:LogicalReasoning skos:closeMatch 5 | MA:0000216 spinal cord UBERON:0002240 spinal cord semapv:LexicalMatching skos:exactMatch 6 | MA:0000142 thymus UBERON:0002370 thymus semapv:LexicalMatching skos:exactMatch 7 | MA:0000129 thyroid gland UBERON:0002046 thyroid gland semapv:LexicalMatching skos:exactMatch 8 | MA:0000072 heart UBERON:0000948 heart semapv:LexicalMatching skos:exactMatch 9 | MA:0000441 trachea UBERON:0003126 trachea semapv:LexicalMatching skos:exactMatch 10 | MA:0000352 esophagus UBERON:0001043 esophagus semapv:LexicalMatching skos:exactMatch 11 | MA:0000415 lung UBERON:0002048 lung semapv:LexicalMatching skos:exactMatch 12 | MA:0000358 liver UBERON:0002107 liver semapv:LexicalMatching skos:exactMatch 13 | MA:0000356 gall bladder UBERON:0002110 gall bladder semapv:LexicalMatching skos:exactMatch 14 | MA:0000353 stomach UBERON:0000945 stomach semapv:LexicalMatching skos:exactMatch 15 | MA:0000337 small intestine UBERON:0002108 small intestine semapv:LexicalMatching skos:exactMatch 16 | MA:0000333 large intestine UBERON:0000059 large intestine semapv:LexicalMatching skos:exactMatch 17 | MA:0000120 pancreas UBERON:0001264 pancreas semapv:LexicalMatching skos:exactMatch 18 | MA:0000141 spleen UBERON:0002106 spleen semapv:LexicalMatching skos:exactMatch 19 | MA:0000368 kidney UBERON:0002113 kidney semapv:LexicalMatching skos:exactMatch 20 | MA:0000116 adrenal gland UBERON:0002369 adrenal gland semapv:LexicalMatching skos:exactMatch 21 | MA:0000139 lymph node UBERON:0000029 lymph node semapv:LexicalMatching skos:exactMatch 22 | MA:0000151 skin UBERON:0002199 integument semapv:LogicalReasoning skos:closeMatch 23 | MA:0003148 skeletal muscle UBERON:0001134 skeletal muscle tissue semapv:LexicalMatching skos:closeMatch 24 | MA:0000380 urinary bladder UBERON:0001255 urinary bladder semapv:LexicalMatching skos:exactMatch 25 | MA:0000145 mammary gland UBERON:0001911 mammary gland semapv:LexicalMatching skos:exactMatch 26 | MA:0000411 testis UBERON:0000473 testis semapv:LexicalMatching skos:exactMatch 27 | MA:0000397 epididymis UBERON:0001301 epididymis semapv:LexicalMatching skos:exactMatch 28 | MA:0000404 prostate gland UBERON:0002367 prostate gland semapv:LexicalMatching skos:exactMatch 29 | MA:0000410 seminal vesicle UBERON:0000998 seminal vesicle semapv:LexicalMatching skos:exactMatch 30 | MA:0000384 ovary UBERON:0000992 ovary semapv:LexicalMatching skos:exactMatch 31 | MA:0000389 uterus UBERON:0000995 uterus semapv:LexicalMatching skos:exactMatch 32 | MA:0000346 salivary gland UBERON:0001044 saliva-secreting gland semapv:LexicalMatching skos:closeMatch 33 | MA:0001331 sternum UBERON:0000975 sternum semapv:LexicalMatching skos:exactMatch 34 | MA:0001359 femur UBERON:0000981 femur semapv:LexicalMatching skos:exactMatch 35 | MA:0000134 bone marrow UBERON:0002371 bone marrow semapv:LexicalMatching skos:exactMatch 36 | MA:0000057 brown adipose tissue UBERON:0001348 brown adipose tissue semapv:LexicalMatching skos:exactMatch 37 | MA:0001361 tibia UBERON:0000979 tibia semapv:LexicalMatching skos:exactMatch 38 | MA:0000471 knee joint UBERON:0001485 knee joint semapv:LexicalMatching skos:exactMatch 39 | MA:0001080 trigeminal V ganglion UBERON:0001675 trigeminal ganglion semapv:LexicalMatching skos:closeMatch 40 | MA:0000284 nasal cavity UBERON:0001707 nasal cavity semapv:LexicalMatching skos:exactMatch 41 | MA:0000236 ear UBERON:0001690 ear semapv:LexicalMatching skos:exactMatch 42 | MA:0000348 tooth UBERON:0001091 calcareous tooth semapv:LexicalMatching skos:closeMatch 43 | MA:0000347 tongue UBERON:0001723 tongue semapv:LexicalMatching skos:exactMatch 44 | MA:0001172 sciatic nerve UBERON:0001322 sciatic nerve semapv:LexicalMatching skos:exactMatch 45 | MA:0001459 bone UBERON:0002481 bone tissue semapv:LexicalMatching skos:closeMatch 46 | MA:0000176 pituitary gland UBERON:0000007 pituitary gland semapv:LexicalMatching skos:exactMatch 47 | MA:0000473 subcutaneous adipose tissue UBERON:0002190 subcutaneous adipose tissue semapv:LexicalMatching skos:exactMatch 48 | MA:0000058 white adipose tissue UBERON:0001347 white adipose tissue semapv:LexicalMatching skos:exactMatch 49 | -------------------------------------------------------------------------------- /sources/impc/sssom/impc_pat_003_mp_terms_30_oct_2020.tsv: -------------------------------------------------------------------------------- 1 | subject_id subject_label object_id object_label mapping_justification predicate_id reviewer_id 2 | MP:0002152 abnormal brain morphology HP:0012443 Abnormality of brain morphology semapv:LexicalMatching skos:exactMatch orcid:0000-0002-7356-1779 3 | MP:0001891 hydroencephaly HP:0000238 Hydrocephalus semapv:LexicalMatching skos:closeMatch 4 | MP:0000774 decreased brain size HP:0007058 Generalized cerebral atrophy/hypoplasia semapv:LogicalReasoning skos:closeMatch 5 | MP:0005238 increased brain size HP:0001355 Megalencephaly semapv:LogicalReasoning skos:closeMatch 6 | MP:0002092 abnormal eye morphology HP:0012372 Abnormal eye morphology semapv:LexicalMatching skos:closeMatch 7 | MP:0001293 anophthalmia HP:0000528 Anophthalmia semapv:LexicalMatching skos:closeMatch 8 | MP:0001297 microphthalmia HP:0000568 Microphthalmia semapv:LexicalMatching skos:exactMatch 9 | MP:0001296 macrophthalmia HP:0001090 Abnormally large globe semapv:LogicalReasoning skos:closeMatch 10 | MP:0001330 abnormal optic nerve morphology HP:0000587 Abnormality of the optic nerve semapv:LogicalReasoning skos:closeMatch 11 | MP:0001333 absent optic nerve HP:0012521 Optic nerve aplasia semapv:LogicalReasoning skos:closeMatch 12 | MP:0006221 optic nerve hypoplasia HP:0000609 Optic nerve hypoplasia semapv:LexicalMatching skos:closeMatch 13 | MP:0008529 enlarged optic nerve sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 14 | MP:000095 abnormal spinal cord morphology HP:0002143 Abnormality of the spinal cord semapv:LexicalMatching skos:closeMatch 15 | MP:0000703 abnormal thymus morphology HP:0000777 Abnormality of the thymus semapv:LexicalMatching skos:closeMatch 16 | MP:0000705 athymia HP:0005359 Aplasia of the thymus semapv:LogicalReasoning skos:closeMatch 17 | MP:0000706 small thymus HP:0000778 Hypoplasia of the thymus semapv:LogicalReasoning skos:closeMatch 18 | MP:0000709 enlarged thymus HP:0010516 Thymus hyperplasia semapv:LogicalReasoning skos:closeMatch 19 | MP:0000681 abnormal thyroid gland morphology HP:0011772 Abnormality of thyroid morphology semapv:LexicalMatching skos:closeMatch 20 | MP:0005314 absent thyroid gland HP:0008191 Thyroid agenesis semapv:LogicalReasoning skos:closeMatch 21 | MP:0002951 small thyroid gland HP:0005990 Thyroid hypoplasia semapv:LogicalReasoning skos:closeMatch 22 | MP:0005355 enlarged thyroid gland HP:0008249 Thyroid hyperplasia semapv:LogicalReasoning skos:closeMatch 23 | MP:0000266 abnormal heart morphology HP:0001654 Abnormal heart morphology semapv:LexicalMatching skos:closeMatch 24 | MP:0006065 abnormal heart position or orientation HP:0004307 Abnormal anatomic location of the heart semapv:LogicalReasoning skos:closeMatch 25 | MP:0002188 small heart HP:0001961 Hypoplastic heart semapv:LogicalReasoning skos:closeMatch 26 | MP:0008725 enlarged heart atrium HP:0031295 Left atrial enlargement semapv:LogicalReasoning skos:closeMatch 27 | MP:0008725 enlarged heart atrium HP:0030718 Right atrial enlargement semapv:LogicalReasoning skos:closeMatch 28 | MP:0000274 enlarged heart HP:0001640 Cardiomegaly semapv:LogicalReasoning skos:closeMatch 29 | MP:0002282 abnormal trachea morphology HP:0002778 Abnormal trachea morphology semapv:LexicalMatching skos:closeMatch 30 | MP:0004549 small trachea HP:0100682 Tracheal atresia semapv:LogicalReasoning skos:closeMatch 31 | MP:0003321 tracheoesophageal fistula HP:0002575 Tracheoesophageal fistula semapv:LexicalMatching skos:closeMatch 32 | MP:0012672 enlarged trachea HP:0010778 Tracheomegaly semapv:LogicalReasoning skos:closeMatch 33 | MP:0000467 abnormal esophagus morphology HP:0002031 Abnormal esophagus morphology semapv:LexicalMatching skos:closeMatch 34 | MP:0010880 small esophagus HP:0002032 Esophageal atresia semapv:LogicalReasoning skos:closeMatch 35 | MP:0004545 enlarged esophagus sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 36 | MP:0001175 abnormal lung morphology HP:0002088 Abnormal lung morphology semapv:LexicalMatching skos:closeMatch 37 | MP:0001181 absent lung HP:0006703 Aplasia/Hypoplasia of the lungs semapv:LogicalReasoning skos:closeMatch 38 | MP:0003641 small lung HP:0006703 Aplasia/Hypoplasia of the lungs semapv:LogicalReasoning skos:closeMatch 39 | MP:0004882 enlarged lung sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 40 | MP:0000598 abnormal liver morphology HP:0410042 Abnormal liver morphology semapv:LexicalMatching skos:closeMatch 41 | MP:0011877 absent liver HP:0100839 Hepatic agenesis semapv:LogicalReasoning skos:closeMatch 42 | MP:0000601 small liver sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 43 | MP:0000599 enlarged liver HP:0002240 Hepatomegaly semapv:LogicalReasoning skos:closeMatch 44 | MP:0005084 abnormal gall bladder morphology HP:0012437 Abnormal gallbladder morphology semapv:LexicalMatching skos:closeMatch 45 | MP:0003250 absent gall bladder HP:0011467 Absent gallbladder semapv:LexicalMatching skos:closeMatch 46 | MP:0005675 small gall bladder HP:0005233 Hypoplasia of the gallbladder semapv:LogicalReasoning skos:closeMatch 47 | MP:0009342 enlarged gall bladder sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 48 | MP:0000470 abnormal stomach morphology HP:0002577 Abnormality of the stomach semapv:LogicalReasoning skos:closeMatch 49 | MP:0011875 absent stomach sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 50 | MP:0002691 small stomach HP:0100841 Microgastria semapv:LogicalReasoning skos:closeMatch 51 | MP:0003883 enlarged stomach HP:0005207 Gastic hypertrophy semapv:LogicalReasoning skos:closeMatch 52 | MP:0003271 abnormal duodenum morphology HP:0030992 Abnormality of the duodenum semapv:LexicalMatching skos:closeMatch 53 | MP:0011880 absent duodenum HP:0002247 Duodenal atresia semapv:LogicalReasoning skos:closeMatch 54 | MP:0011882 enlarged duodenum sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 55 | MP:0003294 intussusception HP:0002576 Intussusception semapv:LogicalReasoning skos:closeMatch 56 | MP:0004002 abnormal jejunum morphology HP:0005265 Abnormality of the jejunum semapv:LogicalReasoning skos:closeMatch 57 | MP:0000498 absent jejunum HP:0005235 Jejunal atresia semapv:LogicalReasoning skos:closeMatch 58 | MP:0011503 distended jejunum sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 59 | MP:0002581 abnormal ileum morphology HP:0001549 Abnormal ileum morphology semapv:LogicalReasoning skos:closeMatch 60 | MP:0000499 absent ileum HP:0011102 Ileal atresia semapv:LogicalReasoning skos:closeMatch 61 | MP:0009483 enlarged ileum sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 62 | MP:0000494 abnormal cecum morphology sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 63 | MP:0009000 absent cecum sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 64 | MP:0009477 small cecum sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 65 | MP:0009476 enlarged cecum sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 66 | MP:0000495 abnormal colon morphology HP:0002250 Abnormal large intestine morphology semapv:LexicalMatching skos:closeMatch 67 | MP:0011884 absent colon HP:0500027 Aplastic colon semapv:LogicalReasoning skos:closeMatch 68 | MP:0003296 microcolon HP:0004388 Microcolon semapv:LexicalMatching skos:closeMatch 69 | MP:0002731 megacolon sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 70 | MP:0000492 abnormal rectum morphology HP:0002034 Abnormality of the rectum semapv:LexicalMatching skos:closeMatch 71 | MP:0009509 absent rectum HP:0025023 Rectal atresia semapv:LogicalReasoning skos:closeMatch 72 | MP:0000493 rectal prolapse HP:0002035 Rectal prolapse semapv:LexicalMatching skos:closeMatch 73 | MP:0003318 rectoperineal fistula HP:0004792 Rectoperineal fistula semapv:LexicalMatching skos:closeMatch 74 | MP:0003320 rectovaginal fistula HP:0000143 Rectovaginal fistula semapv:LexicalMatching skos:closeMatch 75 | MP:0001944 abnormal pancreas morphology HP:0012090 Abnormal pancreas morphology semapv:LexicalMatching skos:closeMatch 76 | MP:0003655 absent pancreas HP:0100801 Pancreatic aplasia semapv:LogicalReasoning skos:closeMatch 77 | MP:0004247 small pancreas HP:0002594 Pancreatic hypoplasia semapv:LogicalReasoning skos:closeMatch 78 | MP:0003450 enlarged pancreas HP:0006277 Pancreatic hyperplasia semapv:LogicalReasoning skos:closeMatch 79 | MP:0000689 abnormal spleen morphology HP:0025408 Abnormal spleen morphology semapv:LexicalMatching skos:closeMatch 80 | MP:0000690 absent spleen HP:0001746 Asplenia semapv:LogicalReasoning skos:closeMatch 81 | MP:0000692 small spleen HP:0006270 Hypoplastic spleen semapv:LogicalReasoning skos:closeMatch 82 | MP:0000691 enlarged spleen HP:0001744 Splenomegaly semapv:LogicalReasoning skos:closeMatch 83 | MP:0002135 abnormal kidney morphology HP:0012210 Abnormal renal morphology semapv:LexicalMatching skos:closeMatch 84 | MP:0003604 single kidney HP:0000122 Unilateral renal agenesis semapv:LogicalReasoning skos:closeMatch 85 | MP:0003068 enlarged kidney HP:0000105 Enlarged kidney semapv:LexicalMatching skos:closeMatch 86 | MP:0002989 small kidney HP:0000089 Renal hypoplasia semapv:LogicalReasoning skos:closeMatch 87 | MP:0008528 polycystic kidney HP:0000113 Polycystic kidney dysplasia semapv:LexicalMatching skos:closeMatch 88 | MP:0000639 abnormal adrenal gland morphology HP:0011732 Abnormality of adrenal morphology semapv:LexicalMatching skos:closeMatch 89 | MP:0005313 absent adrenal gland HP:0011743 Adrenal gland agenesis semapv:LexicalMatching skos:closeMatch 90 | MP:0002768 small adrenal glands HP:0000835 Adrenal hypoplasia semapv:LexicalMatching skos:closeMatch 91 | MP:0000642 enlarged adrenal glands HP:0008221 Adrenal hyperplasia semapv:LexicalMatching skos:closeMatch 92 | MP:0000627 abnormal mammary gland morphology sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 93 | MP:0000629 absent mammary gland HP:0100783 Breast aplasia semapv:LogicalReasoning skos:closeMatch 94 | MP:0009721 supernumerary mammary glands sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 95 | MP:0002339 abnormal lymph node morphology HP:0002733 Abnormality of the lymph nodes semapv:LexicalMatching skos:closeMatch 96 | MP:0008024 absent lymph nodes sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 97 | MP:0002217 small lymph nodes HP:0002732 Lymph node hypoplasia semapv:LogicalReasoning skos:closeMatch 98 | MP:0002219 decreased lymph node number sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 99 | MP:0000702 enlarged lymph nodes HP:0002716 Lymphadenopathy semapv:LogicalReasoning skos:closeMatch 100 | MP:0002060 abnormal skin morphology HP:0011121 Abnormality of skin morphology semapv:LexicalMatching skos:closeMatch 101 | MP:0001199 thin skin HP:0000963 Thin skin semapv:LexicalMatching skos:closeMatch 102 | MP:0001200 thick skin HP:0001072 Thickened skin semapv:LexicalMatching skos:closeMatch 103 | MP:0001192 scaly skin HP:0040189 Scaling skin semapv:LexicalMatching skos:closeMatch 104 | MP:0001211 wrinkled skin HP:0007392 Excessive wrinkled skin semapv:LexicalMatching skos:closeMatch 105 | MP:0000759 abnormal skeletal muscle morphology HP:0011805 Abnormal skeletal muscle morphology semapv:LexicalMatching skos:closeMatch 106 | MP:0004819 decreased skeletal muscle mass HP:0001460 Aplasia/Hypoplasia involving the skeletal musculature semapv:LogicalReasoning skos:closeMatch 107 | MP:0004818 increased skeletal muscle mass HP:0003712 Skeletal muscle hypertrophy semapv:LogicalReasoning skos:closeMatch 108 | MP:0000538 abnormal urinary bladder morphology HP:0025487 Abnormality of bladder morphology semapv:LexicalMatching skos:closeMatch 109 | MP:0009252 absent urinary bladder HP:0010476 Aplasia/Hypoplasia of the bladder semapv:LogicalReasoning skos:closeMatch 110 | MP:0009552 urinary bladder obstruction HP:0041047 Bladder outlet obstruction semapv:LexicalMatching skos:closeMatch 111 | MP:0011625 cystolithiasis HP:0010474 Bladder stones semapv:LogicalReasoning skos:closeMatch 112 | MP:0011874 enlarged urinary bladder HP:0008635 Hypertrophy of the urinary bladder semapv:LogicalReasoning skos:closeMatch 113 | MP:0001146 abnormal testis morphology HP:0000035 Abnormal testis morphology semapv:LexicalMatching skos:closeMatch 114 | MP:0001148 enlarged testes HP:0000053 Macroorchidism semapv:LogicalReasoning skos:closeMatch 115 | MP:0001147 small testis HP:0008734 Decreased testicular size semapv:LogicalReasoning skos:closeMatch 116 | MP:0006415 absent testes HP:0010469 Absent testis semapv:LexicalMatching skos:closeMatch 117 | MP:0002286 cryptorchism HP:0000028 Cryptorchidism semapv:LexicalMatching skos:closeMatch 118 | MP:0002631 abnormal epididymis morphology HP:0009714 Abnormality of the epididymis semapv:LexicalMatching skos:closeMatch 119 | MP:0004727 absent epididymus sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 120 | MP:0004930 small epididymus sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 121 | MP:0004931 enlarged epididymus sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 122 | MP:0001158 abnormal prostate gland morphology HP:0008775 Abnormal prostate morphology semapv:LexicalMatching skos:closeMatch 123 | MP:0001159 absent prostate gland sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 124 | MP:0004958 enlarged prostate gland HP:0008711 Benign prostatic hyperplasia semapv:LogicalReasoning skos:closeMatch 125 | MP:0002774 small prostate gland HP:0008687 Hypoplasia of the prostate semapv:LogicalReasoning skos:closeMatch 126 | MP:0002059 abnormal seminal vesicle morphology sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 127 | MP:0003642 absent seminal vesicle sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 128 | MP:0002997 enlarged seminal vesicle sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 129 | MP:0001157 small seminal vesicle sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 130 | MP:0001126 abnormal ovary morphology HP:0031065 Abnormal ovarian morphology semapv:LexicalMatching skos:closeMatch 131 | MP:0003578 absent ovary HP:0010463 Aplasia of the ovary semapv:LogicalReasoning skos:closeMatch 132 | MP:0001127 small ovary HP:0009724 Hypoplasia of the ovary semapv:LogicalReasoning skos:closeMatch 133 | MP:0004832 enlarged ovary HP:0100879 Enlarged ovaries semapv:LexicalMatching skos:closeMatch 134 | MP:0001102 abnormal uterus morphology HP:0031105 Abnormal uterus morphology semapv:LexicalMatching skos:closeMatch 135 | MP:0003558 absent uterus HP:0000151 Aplasia of the uterus semapv:LogicalReasoning skos:closeMatch 136 | MP:0002637 small uterus HP:0000013 Hypoplasia of the uterus semapv:LogicalReasoning skos:closeMatch 137 | MP:0004906 enlarged uterus HP:0100878 Enlarged uterus semapv:LexicalMatching skos:closeMatch 138 | MP:0009084 blind uterus sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 139 | MP:0009709 hydrometra sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 140 | MP:0000613 abnormal salivary gland morphology HP:0010286 Abnormal salivary gland morphology semapv:LexicalMatching skos:closeMatch 141 | MP:0000614 absent salivary gland sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 142 | MP:0000618 small salivary gland sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 143 | MP:0009516 enlarged salivary gland sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 144 | MP:0000157 abnormal sternum morphology HP:0000766 Abnormality of the sternum semapv:LexicalMatching skos:closeMatch 145 | MP:0000158 absent sternum HP:0010308 Asternia semapv:LogicalReasoning skos:closeMatch 146 | MP:0004321 short sternum HP:0000879 Short sternum semapv:LexicalMatching skos:closeMatch 147 | MP:0012279 wide sternum sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 148 | MP:0004320 split sternum HP:0010309 Bifid sternum semapv:LogicalReasoning skos:closeMatch 149 | MP:0000559 abnormal femur morphology HP:0002823 Abnormality of femur morphology semapv:LexicalMatching skos:closeMatch 150 | MP:0004349 absent femur HP:0012274 Femoral aplasia semapv:LogicalReasoning skos:closeMatch 151 | MP:0004348 long femur sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 152 | MP:0003109 short femur HP:0003097 Short femur semapv:LexicalMatching skos:closeMatch 153 | MP:0002397 abnormal bone marrow morphology HP:0005561 Abnormality of bone marrow cell morphology semapv:LexicalMatching skos:closeMatch 154 | MP:0000558 abnormal tibia morphology HP:0002992 Abnormality of tibia morphology semapv:LexicalMatching skos:closeMatch 155 | MP:0002728 absent tibia HP:0009556 Absent tibia semapv:LexicalMatching skos:closeMatch 156 | MP:0004357 long tibia HP:0010504 Increased length of the tibia semapv:LexicalMatching skos:closeMatch 157 | MP:0002764 short tibia HP:0005736 Short tibia semapv:LexicalMatching skos:closeMatch 158 | MP:0002932 abnormal joint morphology HP:0001367 Abnormal joint morphology semapv:LexicalMatching skos:closeMatch 159 | MP:0003189 fused joints HP:0100240 Synostosis of joints semapv:LogicalReasoning skos:closeMatch 160 | MP:0001092 abnormal trigeminal ganglion morphology HP:0410016 Abnormality of cranial ganglion semapv:LexicalMatching skos:closeMatch 161 | MP:0001095 enlarged trigeminal ganglion sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 162 | MP:0001093 small trigeminal ganglion sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 163 | MP:0002237 abnormal nasal cavity morphology HP:0010640 Abnormality of the nasal cavity semapv:LexicalMatching skos:closeMatch 164 | MP:0002102 abnormal ear morphology HP:0031703 Abnormal ear morphology semapv:LexicalMatching skos:closeMatch 165 | MP:0003678 absent ear lobes sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 166 | MP:0000017 big ears HP:0000400 Macrotia semapv:LogicalReasoning skos:closeMatch 167 | MP:0000018 small ears HP:0008551 Microtia semapv:LogicalReasoning skos:closeMatch 168 | MP:0002689 abnormal molar morphology HP:0011070 Abnormality of molar morphology semapv:LexicalMatching skos:closeMatch 169 | MP:0005358 anbornormal incisor morphology HP:0011063 Abnormality of incisor morphology semapv:LexicalMatching skos:closeMatch 170 | MP:0013129 abnormal tooth colour HP:0011073 Abnormality of dental color semapv:LexicalMatching skos:closeMatch 171 | MP:0000762 abnormal tongue morphology HP:0030809 Abnormal tongue morphology semapv:LexicalMatching skos:closeMatch 172 | MP:0009905 absent tongue HP:0010295 Aplasia/Hypoplasia of the tongue semapv:LogicalReasoning skos:closeMatch 173 | MP:0009907 decreased tongue size HP:0000171 Microglossia semapv:LogicalReasoning skos:closeMatch 174 | MP:0009906 increased tongue size HP:0000158 Macroglossia semapv:LogicalReasoning skos:closeMatch 175 | MP:0002651 abnormal sciatic nerve morphology HP:0045010 Abnormality of peripheral nerves semapv:LogicalReasoning skos:closeMatch 176 | MP:0003795 abnormal bone structure sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 177 | MP:0000633 abnormal pituitary gland morphology HP:0012503 Abnormality of the pituitary gland semapv:LexicalMatching skos:closeMatch 178 | MP:0000636 enlarged pituitary gland HP:0012505 Enlarged pituitary gland semapv:LexicalMatching skos:closeMatch 179 | MP:0005361 small pituitary gland HP:0012506 Small pituitary gland semapv:LexicalMatching skos:closeMatch 180 | MP:0005315 absent pituitary gland HP:0410279 Atrophic parotid gland semapv:LogicalReasoning skos:closeMatch 181 | MP:0011156 abnormal hypodermis fat layer morphology sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 182 | MP:0008844 decreased subcutaneous adipose tissue amount HP:0003758 Reduced subcutaneous fat semapv:LogicalReasoning skos:closeMatch 183 | MP:0010934 increased subcutaneous adipose tissue amount HP:0009003 Increased subcutaneous truncal adipose tissue semapv:LogicalReasoning skos:closeMatch 184 | MP:0002970 abnormal white adipose tissue morphology sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 185 | MP:0001783 decreased white adipose tissue amount HP:0025128 Reduced intraabdominal adipose tissue semapv:LogicalReasoning skos:closeMatch 186 | MP:0001782 increased white adipose tissue amount HP:0008993 Increased intraabdominal fat semapv:LogicalReasoning skos:closeMatch 187 | MP:0002971 abnormal brown fat morphology sssom:NoTermFound No Term Found semapv:ManualMappingCuration skos:closeMatch 188 | MP:0007180 decreased brown fat amount HP:0005995 Decreased adipose tissue around neck semapv:LogicalReasoning skos:closeMatch 189 | MP:0000005 increased brown fat amount HP:0000468 Increased adipose tissue around neck semapv:LogicalReasoning skos:closeMatch 190 | -------------------------------------------------------------------------------- /sources/impc/sssom/impc_pat_003_pato_terms_30_oct_2020.tsv: -------------------------------------------------------------------------------- 1 | subject_id subject_label object_id object_label mapping_justification predicate_id reviewer_id comment 2 | PATO:0000627 focal HP:0030650 Focal semapv:LexicalMatching skos:exactMatch orcid:0000-0002-7356-1779 What is the purpose of this entire table? 3 | PATO:0001791 multifocal (preferred synonym of multi-localised) HP:0030651 Multifocal semapv:LexicalMatching skos:closeMatch 4 | PATO:0002402 multifocal to coalescing HP:0030651 Multifocal semapv:LogicalReasoning skos:closeMatch 5 | PATO:0001566 diffuse HP:0020034 Diffuse semapv:LexicalMatching skos:closeMatch 6 | PATO:0000632 symmetrical sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 7 | PATO:0002401 random pattern sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 8 | PATO:0000634 unilateral HP:0012833 Unilateral semapv:LexicalMatching skos:closeMatch 9 | PATO:0000618 bilateral HP:0012832 Bilateral semapv:LexicalMatching skos:closeMatch 10 | PATO:0000366 left HP:0012835 Left semapv:LexicalMatching skos:closeMatch 11 | PATO:0000367 right HP:0012834 Right semapv:LexicalMatching skos:closeMatch 12 | PATO:0000586 increased size sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 13 | PATO:0000587 decreased size sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 14 | PATO:0000573 increased length sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 15 | PATO:0000574 decreased length sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 16 | PATO:0000411 circular sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 17 | PATO:0001891 ovate sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 18 | PATO:0000407 flat sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 19 | PATO:0001369 raised sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 20 | PATO:0002416 sunken sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 21 | PATO:0000387 soft sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 22 | PATO:0000386 hard sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 23 | PATO:0002406 friable sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 24 | PATO:0002376 inflated sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 25 | PATO:0002409 fluid-filled sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 26 | PATO:0002408 watery sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 27 | PATO:0000322 red sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 28 | PATO:0000317 black sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 29 | PATO:0000952 brown sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 30 | PATO:0000954 pink sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 31 | PATO:0000950 grey sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 32 | PATO:0000323 white sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 33 | PATO:0002410 beige sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 34 | PATO:0000318 blue sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 35 | PATO:0000320 green sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 36 | PATO:0000324 yellow sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 37 | PATO:0002274 mottled sssom:NoTermFound semapv:ManualMappingCuration skos:closeMatch 38 | -------------------------------------------------------------------------------- /sources/impc/sssom/impc_xry_003_mp_terms_30_oct_2020.tsv: -------------------------------------------------------------------------------- 1 | subject_id subject_label object_id object_label mapping_justification predicate_id reviewer_id 2 | MP:0000438 abnormal cranium morphology HP:0002648 Abnormality of calvarial morphology semapv:LexicalMatching skos:closeMatch 3 | MP:0005270 abnormal zygomatic bone morphology HP:0010668 Abnormality of the zygomatic bone semapv:LexicalMatching skos:exactMatch orcid:0000-0002-7356-1779 4 | MP:0000455 abnormal maxilla morphology HP:0000326 Abnormality of the maxilla semapv:LexicalMatching skos:closeMatch 5 | MP:0000458 abnormal mandible morphology HP:0000277 Abnormality of the mandible semapv:LexicalMatching skos:closeMatch 6 | MP:0002100 abnormal tooth morphology HP:0006482 Abnormality of dental morphology semapv:LogicalReasoning skos:closeMatch 7 | MP:0000150 abnormal rib morphology HP:0001547 Abnormality of the rib cage semapv:LogicalReasoning skos:closeMatch 8 | MP:0010099 abnormal thoracic cage shape HP:0001547 Abnormality of the rib cage semapv:LogicalReasoning skos:closeMatch 9 | MP:0000154 rib fusion HP:0000902 Rib fusion semapv:LexicalMatching skos:closeMatch 10 | MP:0000480 increased rib number sssom:NoTermFound No term found semapv:ManualMappingCuration skos:closeMatch 11 | MP:0003345 decreased rib number HP:0000921 Missing ribs semapv:LogicalReasoning skos:closeMatch 12 | MP:0000480 increased rib number sssom:NoTermFound No term found semapv:ManualMappingCuration skos:closeMatch 13 | MP:0003345 decreased rib number HP:0000921 Missing ribs semapv:LogicalReasoning skos:closeMatch 14 | MP:0003048 abnormal cervical vertebrae morphology HP:0003468 Abnormal vertebral morphology semapv:LexicalMatching skos:closeMatch 15 | MP:0004599 abnormal vertebral arch morphology HP:0008438 Vertebral arch anomaly semapv:LexicalMatching skos:closeMatch 16 | MP:0010100 increased cervical vertebrae number HP:0002946 Supernumerary vertebrae semapv:LogicalReasoning skos:closeMatch 17 | MP:0004646 decreased cervical vertebrae number HP:0030305 Decreased number of vertebrae semapv:LexicalMatching skos:closeMatch 18 | MP:0003047 abnormal thoracic vertebrae morphology HP:0003468 Abnormal vertebral morphology semapv:LexicalMatching skos:closeMatch 19 | MP:0004599 abnormal vertebral arch morphology HP:0008438 Vertebral arch anomaly semapv:LexicalMatching skos:closeMatch 20 | MP:0004651 increased thoracic vertebrae number HP:0002946 Supernumerary vertebrae semapv:LogicalReasoning skos:closeMatch 21 | MP:0004648 decreased thoracic vertebrae number HP:0030305 Decreased number of vertebrae semapv:LexicalMatching skos:closeMatch 22 | MP:0003049 abnormal lumbar vertebrae morphology HP:0003468 Abnormal vertebral morphology semapv:LexicalMatching skos:closeMatch 23 | MP:0004599 abnormal vertebral arch morphology HP:0008438 Vertebral arch anomaly semapv:LexicalMatching skos:closeMatch 24 | MP:0004650 increased lumbar vertebrae number HP:0002946 Supernumerary vertebrae semapv:LogicalReasoning skos:closeMatch 25 | MP:0004647 decreased lumbar vertebrae number HP:0030305 Decreased number of vertebrae semapv:LexicalMatching skos:closeMatch 26 | MP:0004599 abnormal vertebral arch morphology HP:0008438 Vertebral arch anomaly semapv:LexicalMatching skos:closeMatch 27 | MP:0010101 increased sacral vertebrae number HP:0002946 Supernumerary vertebrae semapv:LogicalReasoning skos:closeMatch 28 | MP:0004649 decreased sacral vertebrae number HP:0030305 Decreased number of vertebrae semapv:LexicalMatching skos:closeMatch 29 | MP:0002759 abnormal caudal vertebrae morphology HP:0003468 Abnormal vertebral morphology semapv:LexicalMatching skos:closeMatch 30 | MP:0004599 abnormal vertebral arch morphology HP:0008438 Vertebral arch anomaly semapv:LexicalMatching skos:closeMatch 31 | MP:0010102 increased caudal vertebrae number HP:0002946 Supernumerary vertebrae semapv:LogicalReasoning skos:closeMatch 32 | MP:0001539 decreased caudal vertebrae number HP:0030305 Decreased number of vertebrae semapv:LexicalMatching skos:closeMatch 33 | MP:0000137 abnormal vertebrae morphology HP:0003468 Abnormal vertebral morphology semapv:LexicalMatching skos:closeMatch 34 | MP:0004609 vertebral fusion HP:0002948 Vertebral fusion semapv:LexicalMatching skos:closeMatch 35 | MP:0003036 vertebral transformation HP:0003468 Abnormal vertebral morphology semapv:LogicalReasoning skos:closeMatch 36 | MP:0004174 abnormal spine curvature HP:0010674 Abnormality of the curvature of the vertebral column semapv:LogicalReasoning skos:closeMatch 37 | MP:0000161 scoliosis HP:0002650 Scoliosis semapv:LexicalMatching skos:closeMatch 38 | MP:0000160 kyphosis HP:0002808 Kyphosis semapv:LexicalMatching skos:closeMatch 39 | MP:0000162 lordosis HP:0002938 Lumbar hyperlordosis semapv:LogicalReasoning skos:closeMatch 40 | MP:0004613 fusion of vertebral arches HP:0002948 Vertebral fusion semapv:LexicalMatching skos:closeMatch 41 | MP:0004509 abnormal pelvic girdle bone morphology HP:0002644 Abnormality of pelvic girdle bone morphology semapv:LexicalMatching skos:closeMatch 42 | MP:0000149 abnormal scapula morphology HP:0000782 Abnormality of the scapula semapv:LexicalMatching skos:closeMatch 43 | MP:0005298 abnormal clavicle morphology HP:0000889 Abnormality of the clavicle semapv:LexicalMatching skos:closeMatch 44 | MP:0005296 abnormal humerus morphology HP:0031095 Abnormal humerus morphology semapv:LexicalMatching skos:closeMatch 45 | MP:0000552 abnormal radius morphology HP:0045009 Abnormal morphology of the radius semapv:LexicalMatching skos:closeMatch 46 | MP:0005108 abnormal ulna morphology HP:0040071 Abnormal morphology of ulna semapv:LexicalMatching skos:closeMatch 47 | MP:0000559 abnormal femur morphology HP:0002823 Abnormality of femur morphology semapv:LexicalMatching skos:closeMatch 48 | MP:0000558 abnormal tibia morphology HP:0002992 Abnormality of tibia morphology semapv:LexicalMatching skos:closeMatch 49 | MP:0004357 long tibia HP:0002992 Abnormality of tibia morphology semapv:LexicalMatching skos:closeMatch 50 | MP:0002764 short tibia HP:0005736 Short tibia semapv:LexicalMatching skos:closeMatch 51 | MP:0002187 abnormal fibula morphology HP:0002991 Abnormality of fibula morphology semapv:LexicalMatching skos:closeMatch 52 | MP:0002932 abnormal joint morphology HP:0001367 Abnormal joint morphology semapv:LexicalMatching skos:closeMatch 53 | MP:0000562 polydactyly HP:0010442 Polydactyly semapv:LexicalMatching skos:closeMatch 54 | MP:0000565 oligodactyly HP:0012165 Oligodactyly semapv:LexicalMatching skos:closeMatch 55 | MP:0002110 abnormal digit morphology HP:0011297 Abnormal digit morphology semapv:LexicalMatching skos:closeMatch 56 | MP:0000564 syndactyly HP:0001159 Syndactyly semapv:LexicalMatching skos:closeMatch 57 | MP:0004083 polysyndactyly HP:0005817 Postaxial polysyndactyly of foot semapv:LogicalReasoning skos:closeMatch 58 | MP:0002544 brachydactyly HP:0001156 Brachydactyly semapv:LexicalMatching skos:closeMatch 59 | -------------------------------------------------------------------------------- /sources/mgi/mp-ub-em-ma(2017copy).xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mapping-commons/mh_mapping_initiative/ad95b5e6eec7ba0c744c32a684aa22407a324210/sources/mgi/mp-ub-em-ma(2017copy).xlsx -------------------------------------------------------------------------------- /sources/mmhcdb/Apr 2017 MMHCdb, DO, and NCIt tumor terms.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mapping-commons/mh_mapping_initiative/ad95b5e6eec7ba0c744c32a684aa22407a324210/sources/mmhcdb/Apr 2017 MMHCdb, DO, and NCIt tumor terms.xlsx -------------------------------------------------------------------------------- /sources/mmhcdb/MMHCdb tumor terms to NCI Thesaurus (Jan 2019 updated June 2020).xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mapping-commons/mh_mapping_initiative/ad95b5e6eec7ba0c744c32a684aa22407a324210/sources/mmhcdb/MMHCdb tumor terms to NCI Thesaurus (Jan 2019 updated June 2020).xlsx -------------------------------------------------------------------------------- /sources/pistoia/calculated_output_ordo_mp.csv: -------------------------------------------------------------------------------- 1 | sourceIRI,mappedIRI,score,sourceLabel,mappedLabel,NormalizedScore 2 | http://www.orpha.net/ORDO/Orphanet_98613,http://purl.obolibrary.org/obo/MP_0006193,3.0,Conjunctival telangiectasia,conjunctival telangiectasia,0.75 3 | http://www.orpha.net/ORDO/Orphanet_156207,http://purl.obolibrary.org/obo/MP_0009906,3.0,Macroglossia,increased tongue size,0.75 4 | http://www.orpha.net/ORDO/Orphanet_79364,http://purl.obolibrary.org/obo/MP_0000414,3.0,Alopecia,alopecia,0.75 5 | http://www.orpha.net/ORDO/Orphanet_98575,http://purl.obolibrary.org/obo/MP_0030166,3.0,Telecanthus,increased inner canthal distance,0.75 6 | http://www.orpha.net/ORDO/Orphanet_91495,http://purl.obolibrary.org/obo/MP_0010711,3.0,Persistent hyperplastic primary vitreous,persistent hyperplastic primary vitreous,0.75 7 | http://www.orpha.net/ORDO/Orphanet_90025,http://purl.obolibrary.org/obo/MP_0000564,3.0,Syndactyly,syndactyly,0.75 8 | http://www.orpha.net/ORDO/Orphanet_79389,http://purl.obolibrary.org/obo/MP_0003786,3.0,Premature aging,premature aging,0.75 9 | http://www.orpha.net/ORDO/Orphanet_209,http://purl.obolibrary.org/obo/MP_0005421,3.0,Cutis laxa,loose skin,0.75 10 | http://www.orpha.net/ORDO/Orphanet_69,http://purl.obolibrary.org/obo/MP_0000604,3.0,Amyloidosis,amyloidosis,0.75 11 | http://www.orpha.net/ORDO/Orphanet_2130,http://purl.obolibrary.org/obo/MP_0008985,3.0,Hemimelia,hemimelia,0.75 12 | http://www.orpha.net/ORDO/Orphanet_93338,http://purl.obolibrary.org/obo/MP_0004083,3.0,Polysyndactyly,polysyndactyly,0.75 13 | http://www.orpha.net/ORDO/Orphanet_2781,http://purl.obolibrary.org/obo/MP_0000067,3.0,Osteopetrosis,osteopetrosis,0.75 14 | http://www.orpha.net/ORDO/Orphanet_411709,http://purl.obolibrary.org/obo/MP_0000520,3.0,Renal agenesis,absent kidney,0.75 15 | http://www.orpha.net/ORDO/Orphanet_2882,http://purl.obolibrary.org/obo/MP_0010077,3.0,Sitosterolemia,increased phytosterol level,0.75 16 | http://www.orpha.net/ORDO/Orphanet_521,http://purl.obolibrary.org/obo/MP_0005481,3.0,Chronic myeloid leukemia,increased chronic myelocytic leukemia incidence,0.75 17 | http://www.orpha.net/ORDO/Orphanet_79225,http://purl.obolibrary.org/obo/MP_0009589,3.0,Sphingolipidosis,sphingomyelinosis,0.75 18 | http://www.orpha.net/ORDO/Orphanet_214,http://purl.obolibrary.org/obo/MP_0020400,3.0,Cystinuria,cystinuria,0.75 19 | http://www.orpha.net/ORDO/Orphanet_155878,http://purl.obolibrary.org/obo/MP_0011615,3.0,Submucosal cleft palate,submucous cleft palate,0.75 20 | http://www.orpha.net/ORDO/Orphanet_101023,http://purl.obolibrary.org/obo/MP_0013545,3.0,Cleft hard palate,cleft hard palate,0.75 21 | http://www.orpha.net/ORDO/Orphanet_98282,http://purl.obolibrary.org/obo/MP_0009440,3.0,Plasma cell tumor,increased myeloma incidence,0.75 22 | http://www.orpha.net/ORDO/Orphanet_79383,http://purl.obolibrary.org/obo/MP_0003390,3.0,Lymphedema,lymphedema,0.75 23 | http://www.orpha.net/ORDO/Orphanet_79365,http://purl.obolibrary.org/obo/MP_0000412,3.0,Hypertrichosis,excessive hair,0.75 24 | http://www.orpha.net/ORDO/Orphanet_1531,http://purl.obolibrary.org/obo/MP_0000081,3.0,Craniosynostosis,premature cranial suture closure,0.75 25 | http://www.orpha.net/ORDO/Orphanet_167848,http://purl.obolibrary.org/obo/MP_0005330,3.0,Cardiomyopathy,cardiomyopathy,0.75 26 | http://www.orpha.net/ORDO/Orphanet_738,http://purl.obolibrary.org/obo/MP_0005654,3.0,Porphyria,porphyria,0.75 27 | http://www.orpha.net/ORDO/Orphanet_1457,http://purl.obolibrary.org/obo/MP_0003387,3.0,Aorta coarctation,aorta coarctation,0.75 28 | http://www.orpha.net/ORDO/Orphanet_1463,http://purl.obolibrary.org/obo/MP_0010409,3.0,Triatrial heart,cor triatriatum,0.75 29 | http://www.orpha.net/ORDO/Orphanet_1464,http://purl.obolibrary.org/obo/MP_0010432,3.0,Univentricular heart,common ventricle,0.75 30 | http://www.orpha.net/ORDO/Orphanet_77,http://purl.obolibrary.org/obo/MP_0005261,3.0,Aniridia,aniridia,0.75 31 | http://www.orpha.net/ORDO/Orphanet_450,http://purl.obolibrary.org/obo/MP_0004133,3.0,Heterotaxia,heterotaxia,0.75 32 | http://www.orpha.net/ORDO/Orphanet_2695,http://purl.obolibrary.org/obo/MP_0030117,3.0,Bifid nose,bifid nose,0.75 33 | http://www.orpha.net/ORDO/Orphanet_963,http://purl.obolibrary.org/obo/MP_0003506,3.0,Acromegaly,acromegaly,0.75 34 | http://www.orpha.net/ORDO/Orphanet_98427,http://purl.obolibrary.org/obo/MP_0002872,3.0,Polycythemia,polycythemia,0.75 35 | http://www.orpha.net/ORDO/Orphanet_95708,http://purl.obolibrary.org/obo/MP_0003378,3.0,Precocious puberty,early sexual maturation,0.75 36 | http://www.orpha.net/ORDO/Orphanet_755,http://purl.obolibrary.org/obo/MP_0005536,3.0,Leydig cell hypoplasia,Leydig cell hypoplasia,0.75 37 | http://www.orpha.net/ORDO/Orphanet_1671,http://purl.obolibrary.org/obo/MP_0012710,3.0,Diastematomyelia,diastematomyelia,0.75 38 | http://www.orpha.net/ORDO/Orphanet_780,http://purl.obolibrary.org/obo/MP_0002036,3.0,Rhabdomyosarcoma,increased rhabdomyosarcoma incidence,0.75 39 | http://www.orpha.net/ORDO/Orphanet_439167,http://purl.obolibrary.org/obo/MP_0006372,3.0,Placental insufficiency,impaired placental function,0.75 40 | http://www.orpha.net/ORDO/Orphanet_675,http://purl.obolibrary.org/obo/MP_0006261,3.0,Annular pancreas,annular pancreas,0.75 41 | http://www.orpha.net/ORDO/Orphanet_674,http://purl.obolibrary.org/obo/MP_0013291,3.0,Accessory pancreas,ectopic pancreas,0.75 42 | http://www.orpha.net/ORDO/Orphanet_46724,http://purl.obolibrary.org/obo/MP_0010530,3.0,Cerebral arteriovenous malformation,cerebral arteriovenous malformation,0.75 43 | http://www.orpha.net/ORDO/Orphanet_101043,http://purl.obolibrary.org/obo/MP_0002747,3.0,Aortic valve dysplasia,abnormal aortic valve morphology,0.75 44 | http://www.orpha.net/ORDO/Orphanet_2014,http://purl.obolibrary.org/obo/MP_0000111,3.0,Cleft palate,cleft palate,0.75 45 | http://www.orpha.net/ORDO/Orphanet_157769,http://purl.obolibrary.org/obo/MP_0002767,3.0,Situs ambiguus,situs ambiguus,0.75 46 | http://www.orpha.net/ORDO/Orphanet_101063,http://purl.obolibrary.org/obo/MP_0011252,3.0,Situs inversus totalis,situs inversus totalis,0.75 47 | http://www.orpha.net/ORDO/Orphanet_95720,http://purl.obolibrary.org/obo/MP_0003499,3.0,Thyroid hypoplasia,thyroid hypoplasia,0.75 48 | http://www.orpha.net/ORDO/Orphanet_660,http://purl.obolibrary.org/obo/MP_0003052,3.0,Omphalocele,omphalocele,0.75 49 | http://www.orpha.net/ORDO/Orphanet_284804,http://purl.obolibrary.org/obo/MP_0006159,3.0,Ocular albinism,ocular albinism,0.75 50 | http://www.orpha.net/ORDO/Orphanet_93108,http://purl.obolibrary.org/obo/MP_0002135,3.0,Renal dysplasia,abnormal kidney morphology,0.75 51 | http://www.orpha.net/ORDO/Orphanet_1666,http://purl.obolibrary.org/obo/MP_0000644,3.0,Dextrocardia,dextrocardia,0.75 52 | http://www.orpha.net/ORDO/Orphanet_93101,http://purl.obolibrary.org/obo/MP_0003446,3.0,Renal hypoplasia,renal hypoplasia,0.75 53 | http://www.orpha.net/ORDO/Orphanet_199323,http://purl.obolibrary.org/obo/MP_0003665,3.0,Endophthalmitis,endophthalmitis,0.75 54 | http://www.orpha.net/ORDO/Orphanet_2913,http://purl.obolibrary.org/obo/MP_0000562,3.0,Polydactyly,polydactyly,0.75 55 | http://www.orpha.net/ORDO/Orphanet_93,http://purl.obolibrary.org/obo/MP_0011516,3.0,Aspartylglucosaminuria,aspartylglucosaminuria,0.75 56 | http://www.orpha.net/ORDO/Orphanet_180139,http://purl.obolibrary.org/obo/MP_0001121,3.0,Uterine hypoplasia,uterus hypoplasia,0.75 57 | http://www.orpha.net/ORDO/Orphanet_1041,http://purl.obolibrary.org/obo/MP_0002192,3.0,Hydrops fetalis,hydrops fetalis,0.75 58 | http://www.orpha.net/ORDO/Orphanet_263413,http://purl.obolibrary.org/obo/MP_0003667,3.0,Angiosarcoma,increased hemangiosarcoma incidence,0.75 59 | http://www.orpha.net/ORDO/Orphanet_99867,http://purl.obolibrary.org/obo/MP_0014127,3.0,Thymoma,increased thymoma incidence,0.75 60 | http://www.orpha.net/ORDO/Orphanet_52759,http://purl.obolibrary.org/obo/MP_0001864,3.0,Vasculitis,vasculitis,0.75 61 | http://www.orpha.net/ORDO/Orphanet_480501,http://purl.obolibrary.org/obo/MP_0003266,3.0,Choledochal cyst,biliary cyst,0.75 62 | http://www.orpha.net/ORDO/Orphanet_91414,http://purl.obolibrary.org/obo/MP_0002013,3.0,Pilomatrixoma,increased pilomatricoma incidence,0.75 63 | http://www.orpha.net/ORDO/Orphanet_141253,http://purl.obolibrary.org/obo/MP_0008799,3.0,Oblique facial cleft,oblique facial cleft,0.75 64 | http://www.orpha.net/ORDO/Orphanet_141269,http://purl.obolibrary.org/obo/MP_0008798,3.0,Lateral facial cleft,lateral facial cleft,0.75 65 | http://www.orpha.net/ORDO/Orphanet_141229,http://purl.obolibrary.org/obo/MP_0008797,3.0,Facial cleft,facial cleft,0.75 66 | http://www.orpha.net/ORDO/Orphanet_93968,http://purl.obolibrary.org/obo/MP_0012259,3.0,Meningocele,meningocele,0.75 67 | http://www.orpha.net/ORDO/Orphanet_93962,http://purl.obolibrary.org/obo/MP_0030126,3.0,Cervical dystonia,torticollis,0.75 68 | http://www.orpha.net/ORDO/Orphanet_93969,http://purl.obolibrary.org/obo/MP_0009929,3.0,Myelomeningocele,meningomyelocele,0.75 69 | http://www.orpha.net/ORDO/Orphanet_268744,http://purl.obolibrary.org/obo/MP_0012547,3.0,Spina bifida cystica,spina bifida cystica,0.75 70 | http://www.orpha.net/ORDO/Orphanet_93976,http://purl.obolibrary.org/obo/MP_0003142,3.0,Anotia,anotia,0.75 71 | http://www.orpha.net/ORDO/Orphanet_2162,http://purl.obolibrary.org/obo/MP_0005157,3.0,Holoprosencephaly,holoprosencephaly,0.75 72 | http://www.orpha.net/ORDO/Orphanet_93928,http://purl.obolibrary.org/obo/MP_0003598,3.0,Epispadias,epispadia,0.75 73 | http://www.orpha.net/ORDO/Orphanet_141163,http://purl.obolibrary.org/obo/MP_0030328,3.0,Glossopalatine ankylosis,glossopalatal ankylosis,0.75 74 | http://www.orpha.net/ORDO/Orphanet_166415,http://purl.obolibrary.org/obo/MP_0001496,3.0,Audiogenic seizures,audiogenic seizures,0.75 75 | http://www.orpha.net/ORDO/Orphanet_431341,http://purl.obolibrary.org/obo/MP_0011852,3.0,Patent urachus,patent urachus,0.75 76 | http://www.orpha.net/ORDO/Orphanet_97275,http://purl.obolibrary.org/obo/MP_0001847,3.0,Encephalitis,brain inflammation,0.75 77 | http://www.orpha.net/ORDO/Orphanet_123411,http://purl.obolibrary.org/obo/MP_0005638,3.0,hemochromatosis,hemochromatosis,0.75 78 | http://www.orpha.net/ORDO/Orphanet_83463,http://purl.obolibrary.org/obo/MP_0000018,3.0,Microtia,small ears,0.75 79 | http://www.orpha.net/ORDO/Orphanet_3280,http://purl.obolibrary.org/obo/MP_0012545,3.0,Syringomyelia,syringomyelia,0.75 80 | http://www.orpha.net/ORDO/Orphanet_268369,http://purl.obolibrary.org/obo/MP_0012547,3.0,Spina bifida aperta,spina bifida cystica,0.75 81 | http://www.orpha.net/ORDO/Orphanet_99107,http://purl.obolibrary.org/obo/MP_0010450,3.0,Atrial septal aneurysm,atrial septal aneurysm,0.75 82 | http://www.orpha.net/ORDO/Orphanet_65681,http://purl.obolibrary.org/obo/MP_0001144,3.0,Vaginal atresia,vagina atresia,0.75 83 | http://www.orpha.net/ORDO/Orphanet_99083,http://purl.obolibrary.org/obo/MP_0010460,3.0,Pulmonary artery hypoplasia,pulmonary artery hypoplasia,0.75 84 | http://www.orpha.net/ORDO/Orphanet_3426,http://purl.obolibrary.org/obo/MP_0000284,3.0,Double outlet right ventricle,double outlet right ventricle,0.75 85 | http://www.orpha.net/ORDO/Orphanet_99079,http://purl.obolibrary.org/obo/MP_0004161,3.0,Cervical aortic arch,cervical aortic arch,0.75 86 | http://www.orpha.net/ORDO/Orphanet_99081,http://purl.obolibrary.org/obo/MP_0004158,3.0,Right aortic arch,right aortic arch,0.75 87 | http://www.orpha.net/ORDO/Orphanet_363483,http://purl.obolibrary.org/obo/MP_0004478,3.0,Testicular teratoma,increased testicular teratoma incidence,0.75 88 | http://www.orpha.net/ORDO/Orphanet_64720,http://purl.obolibrary.org/obo/MP_0002035,3.0,Leiomyosarcoma,increased leiomyosarcoma incidence,0.75 89 | http://www.orpha.net/ORDO/Orphanet_98715,http://purl.obolibrary.org/obo/MP_0005515,3.0,Uveitis,uveitis,0.75 90 | http://www.orpha.net/ORDO/Orphanet_63260,http://purl.obolibrary.org/obo/MP_0008784,3.0,Craniorachischisis,craniorachischisis,0.75 91 | http://www.orpha.net/ORDO/Orphanet_217604,http://purl.obolibrary.org/obo/MP_0002795,3.0,Dilated cardiomyopathy,dilated cardiomyopathy,0.75 92 | http://www.orpha.net/ORDO/Orphanet_3193,http://purl.obolibrary.org/obo/MP_0010471,3.0,Supravalvular aortic stenosis,supravalvar aortic stenosis,0.75 93 | http://www.orpha.net/ORDO/Orphanet_1077,http://purl.obolibrary.org/obo/MP_0030449,3.0,Dental ankylosis,tooth ankylosis,0.75 94 | http://www.orpha.net/ORDO/Orphanet_2368,http://purl.obolibrary.org/obo/MP_0000757,3.0,Gastroschisis,herniated abdominal wall,0.75 95 | http://www.orpha.net/ORDO/Orphanet_306773,http://purl.obolibrary.org/obo/MP_0005604,3.0,Hyperekplexia,hyperekplexia,0.75 96 | http://www.orpha.net/ORDO/Orphanet_2287,http://purl.obolibrary.org/obo/MP_0030475,3.0,Fused mandibular incisors,fused lower incisors,0.75 97 | http://www.orpha.net/ORDO/Orphanet_1203,http://purl.obolibrary.org/obo/MP_0003272,3.0,Duodenal atresia,duodenal atresia,0.75 98 | http://www.orpha.net/ORDO/Orphanet_95443,http://purl.obolibrary.org/obo/MP_0000650,3.0,Mesocardia,mesocardia,0.75 99 | http://www.orpha.net/ORDO/Orphanet_95448,http://purl.obolibrary.org/obo/MP_0006115,3.0,Aortic valve atresia,aortic valve atresia,0.75 100 | http://www.orpha.net/ORDO/Orphanet_95458,http://purl.obolibrary.org/obo/MP_0006125,3.0,Tricuspid valve prolapse,tricuspid valve prolapse,0.75 101 | http://www.orpha.net/ORDO/Orphanet_1199,http://purl.obolibrary.org/obo/MP_0003276,3.0,Esophageal atresia,esophageal atresia,0.75 102 | http://www.orpha.net/ORDO/Orphanet_1160,http://purl.obolibrary.org/obo/MP_0012080,3.0,Chylous ascites,chylous ascites,0.75 103 | http://www.orpha.net/ORDO/Orphanet_3289,http://purl.obolibrary.org/obo/MP_0030496,3.0,Taurodontism,taurodontia,0.75 104 | http://www.orpha.net/ORDO/Orphanet_448270,http://purl.obolibrary.org/obo/MP_0011660,3.0,Ectopia cordis,ectopia cordis,0.75 105 | http://www.orpha.net/ORDO/Orphanet_3169,http://purl.obolibrary.org/obo/MP_0003445,3.0,Sirenomelia,sirenomelia,0.75 106 | http://www.orpha.net/ORDO/Orphanet_3190,http://purl.obolibrary.org/obo/MP_0010449,3.0,Subpulmonary stenosis,heart right ventricle outflow tract stenosis,0.75 107 | http://www.orpha.net/ORDO/Orphanet_3427,http://purl.obolibrary.org/obo/MP_0010427,3.0,Double outlet left ventricle,double outlet left ventricle,0.75 108 | http://www.orpha.net/ORDO/Orphanet_137914,http://purl.obolibrary.org/obo/MP_0008970,3.0,Choanal atresia,choanal atresia,0.75 109 | http://www.orpha.net/ORDO/Orphanet_96321,http://purl.obolibrary.org/obo/MP_0004025,3.0,Polyploidy,polyploidy,0.75 110 | http://www.orpha.net/ORDO/Orphanet_2038,http://purl.obolibrary.org/obo/MP_0010480,3.0,Pulmonary arteriovenous malformation,pulmonary arteriovenous malformation,0.75 111 | http://www.orpha.net/ORDO/Orphanet_3148,http://purl.obolibrary.org/obo/MP_0002030,0.98734,Malignant peripheral nerve sheath tumor,increased neurofibrosarcoma incidence,0.246835 112 | http://www.orpha.net/ORDO/Orphanet_98722,http://purl.obolibrary.org/obo/MP_0010412,0.98305,Atrioventricular canal defect,atrioventricular septal defect,0.2457625 113 | http://www.orpha.net/ORDO/Orphanet_93100,http://purl.obolibrary.org/obo/MP_0003604,0.98039,"Renal agenesis, unilateral",single kidney,0.2450975 114 | http://www.orpha.net/ORDO/Orphanet_1848,http://purl.obolibrary.org/obo/MP_0000520,0.97959,"Renal agenesis, bilateral",absent kidney,0.2448975 115 | http://www.orpha.net/ORDO/Orphanet_98691,http://purl.obolibrary.org/obo/MP_0001389,0.97674,Abnormal eye movements,abnormal eye movement,0.244185 116 | http://www.orpha.net/ORDO/Orphanet_99054,http://purl.obolibrary.org/obo/MP_0006128,0.96154,Valvular pulmonary stenosis,pulmonary valve stenosis,0.240385 117 | http://www.orpha.net/ORDO/Orphanet_99047,http://purl.obolibrary.org/obo/MP_0011669,0.96,Double outlet right ventricle with doubly committed ventricular septal defect,"double outlet right ventricle, doubly committed ventricular septal defect",0.24 118 | http://www.orpha.net/ORDO/Orphanet_99098,http://purl.obolibrary.org/obo/MP_0010411,0.95455,Cor triatriatum dexter,cor triatriatum dextrum,0.2386375 119 | http://www.orpha.net/ORDO/Orphanet_118246,http://purl.obolibrary.org/obo/MP_0001326,0.95238,retinal degeneration 3,retinal degeneration,0.238095 120 | http://www.orpha.net/ORDO/Orphanet_99097,http://purl.obolibrary.org/obo/MP_0010419,0.95238,Single ventricular septal defect,inlet ventricular septal defect,0.238095 121 | http://www.orpha.net/ORDO/Orphanet_99071,http://purl.obolibrary.org/obo/MP_0010481,0.94915,Aorto-left ventricular tunnel,left ventricle to aorta tunnel,0.2372875 122 | http://www.orpha.net/ORDO/Orphanet_1054,http://purl.obolibrary.org/obo/MP_0010483,0.94545,Aneurysm of sinus of Valsalva,aortic sinus aneurysm,0.2363625 123 | http://www.orpha.net/ORDO/Orphanet_3384,http://purl.obolibrary.org/obo/MP_0002633,0.94444,Truncus arteriosus,persistent truncus arteriosis,0.23611 124 | http://www.orpha.net/ORDO/Orphanet_216675,http://purl.obolibrary.org/obo/MP_0004110,0.93939,Transposition of the great arteries,transposition of great arteries,0.2348475 125 | http://www.orpha.net/ORDO/Orphanet_99099,http://purl.obolibrary.org/obo/MP_0010410,0.93878,Cor triatriatum sinister,cor triatriatum sinistrum,0.234695 126 | http://www.orpha.net/ORDO/Orphanet_98823,http://purl.obolibrary.org/obo/MP_0005481,0.93103,Chronic myelomonocytic leukemia,increased chronic myelocytic leukemia incidence,0.2327575 127 | http://www.orpha.net/ORDO/Orphanet_98653,http://purl.obolibrary.org/obo/MP_0020486,0.93023,Lens position anomaly,abnormal lens topology,0.2325575 128 | http://www.orpha.net/ORDO/Orphanet_98947,http://purl.obolibrary.org/obo/MP_0010716,0.92683,Coloboma of optic disc,optic disc coloboma,0.2317075 129 | http://www.orpha.net/ORDO/Orphanet_99103,http://purl.obolibrary.org/obo/MP_0010405,0.92308,"Atrial septal defect, ostium secundum type",ostium secundum atrial septal defect,0.23077 130 | http://www.orpha.net/ORDO/Orphanet_329931,http://purl.obolibrary.org/obo/MP_0002743,0.92308,C3 glomerulonephritis,glomerulonephritis,0.23077 131 | http://www.orpha.net/ORDO/Orphanet_99104,http://purl.obolibrary.org/obo/MP_0010407,0.92105,"Atrial septal defect, coronary sinus type",coronary sinus atrial septal defect,0.2302625 132 | http://www.orpha.net/ORDO/Orphanet_99106,http://purl.obolibrary.org/obo/MP_0010404,0.91892,"Atrial septal defect, ostium primum type",ostium primum atrial septal defect,0.22973 133 | http://www.orpha.net/ORDO/Orphanet_99105,http://purl.obolibrary.org/obo/MP_0010408,0.91892,"Atrial septal defect, sinus venosus type",sinus venosus atrial septal defect,0.22973 134 | http://www.orpha.net/ORDO/Orphanet_99044,http://purl.obolibrary.org/obo/MP_0011667,0.91852,Double outlet right ventricle with subaortic ventricular septal defect,double outlet right ventricle with atrioventricular septal defect,0.22963 135 | http://www.orpha.net/ORDO/Orphanet_211266,http://purl.obolibrary.org/obo/MP_0006093,0.91228,Rare arteriovenous malformation,arteriovenous malformation,0.22807 136 | http://www.orpha.net/ORDO/Orphanet_105,http://purl.obolibrary.org/obo/MP_0003591,0.90909,Atresia of urethra,urethra atresia,0.2272725 137 | http://www.orpha.net/ORDO/Orphanet_263746,http://purl.obolibrary.org/obo/MP_0004023,0.90566,Y chromosome number anomaly,abnormal chromosome number,0.226415 138 | http://www.orpha.net/ORDO/Orphanet_263714,http://purl.obolibrary.org/obo/MP_0004023,0.90566,X chromosome number anomaly,abnormal chromosome number,0.226415 139 | http://www.orpha.net/ORDO/Orphanet_1138,http://purl.obolibrary.org/obo/MP_0013980,0.90141,Abnormal origin of the pulmonary artery,abnormal pulmonary artery origin,0.2253525 140 | -------------------------------------------------------------------------------- /use_cases/README.md: -------------------------------------------------------------------------------- 1 | # Use cases 2 | 3 | - Kids First: 4 | - Dataset: [Kids First: April2020_KF_Data_Phenotypes_HPO.csv](April2020_KF_Data_Phenotypes_HPO.csv). 5 | - Contact: Deanne Taylor, Ben Stear 6 | - Description: All the unique terms from the "April 2020 positives fixed" sheet (Kids First dataset), a per-subject-phenotype description w/HPO phenotype as a "positive” result as a follow-back w/the clinical diagnosis. This data was repaired from "April 2020 phenodata raw" only for those with an observed "positive." --------------------------------------------------------------------------------