├── .gitignore
├── .travis.yml
├── LICENSE-BSD.md
├── LICENSE-CC0.md
├── README.md
├── config_files
├── CONFIG.md
├── README.md
├── pubtator_central_config.json
├── pubtator_config.json
└── tests_config.json
├── data
├── .gitattributes
├── example
│ ├── 1-sample-annotations.txt
│ ├── 2-sample-docs.xml
│ ├── 3-sample-tags.tsv
│ ├── 4-hetnet-tags.tsv
│ ├── 5-sample-pmids-to-pmcids.tsv
│ ├── 6-sample-full-text.xml
│ ├── 7-sample-full-text-tags.tsv
│ ├── 8-hetnet-full-text-tags.tsv
│ ├── README.md
│ └── ncbi_pmid_to_pmcid_map.tsv.xz
└── temp
│ ├── batch_0.xml
│ ├── batch_1.xml
│ └── batch_log.tsv
├── download
└── bioconcepts2pubtator_offsets.gz.log
├── execute.py
├── mapper
├── drugbank_mapper.tsv
└── map_to_drugbank.py
├── requirements.txt
├── scripts
├── __init__.py
├── download_full_text.py
├── extract_tags.py
├── hetnet_id_extractor.py
├── map_ids.py
├── pubtator_to_xml.py
└── utilities.py
└── tests.sh
/.gitignore:
--------------------------------------------------------------------------------
1 | # Python
2 | __pycache__/
3 | *.pyc
4 |
5 | # Jupyter Notebook
6 | .ipynb_checkpoints
7 |
--------------------------------------------------------------------------------
/.travis.yml:
--------------------------------------------------------------------------------
1 | language: generic
2 | before_install:
3 | - sudo apt-get update --quiet --quiet
4 | - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh --output-document miniconda.sh
5 | - bash miniconda.sh -b -p $HOME/miniconda
6 | - export PATH="$HOME/miniconda/bin:$PATH"
7 | - hash -r
8 | - conda config --set always_yes yes --set changeps1 no
9 | - conda update --quiet conda
10 | - conda info --all
11 | install:
12 | - conda create --name pubtator python=3.8
13 | - source activate pubtator
14 | - pip install -r requirements.txt
15 | script:
16 | - sh tests.sh
17 |
--------------------------------------------------------------------------------
/LICENSE-BSD.md:
--------------------------------------------------------------------------------
1 | # BSD 3-Clause License
2 |
3 | _Copyright © 2017, The Greene Lab at the University of Pennsylvania_
4 |
5 | _All rights reserved._
6 |
7 | Redistribution and use in source and binary forms, with or without
8 | modification, are permitted provided that the following conditions are met:
9 |
10 | 1. Redistributions of source code must retain the above copyright notice, this
11 | list of conditions and the following disclaimer.
12 |
13 | 2. Redistributions in binary form must reproduce the above copyright notice,
14 | this list of conditions and the following disclaimer in the documentation
15 | and/or other materials provided with the distribution.
16 |
17 | 3. Neither the name of the copyright holder nor the names of its contributors
18 | may be used to endorse or promote products derived from this software without
19 | specific prior written permission.
20 |
21 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
22 | ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
23 | WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
24 | DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
25 | FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
26 | DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
27 | SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
28 | CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
29 | OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
30 | OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
31 |
--------------------------------------------------------------------------------
/LICENSE-CC0.md:
--------------------------------------------------------------------------------
1 | # CC0 1.0 Universal
2 |
3 | ```
4 | CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS INFORMATION ON AN "AS-IS" BASIS. CREATIVE COMMONS MAKES NO WARRANTIES REGARDING THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED HEREUNDER, AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED HEREUNDER.
5 | ```
6 |
7 | ### Statement of Purpose
8 |
9 | The laws of most jurisdictions throughout the world automatically confer exclusive Copyright and Related Rights (defined below) upon the creator and subsequent owner(s) (each and all, an "owner") of an original work of authorship and/or a database (each, a "Work").
10 |
11 | Certain owners wish to permanently relinquish those rights to a Work for the purpose of contributing to a commons of creative, cultural and scientific works ("Commons") that the public can reliably and without fear of later claims of infringement build upon, modify, incorporate in other works, reuse and redistribute as freely as possible in any form whatsoever and for any purposes, including without limitation commercial purposes. These owners may contribute to the Commons to promote the ideal of a free culture and the further production of creative, cultural and scientific works, or to gain reputation or greater distribution for their Work in part through the use and efforts of others.
12 |
13 | For these and/or other purposes and motivations, and without any expectation of additional consideration or compensation, the person associating CC0 with a Work (the "Affirmer"), to the extent that he or she is an owner of Copyright and Related Rights in the Work, voluntarily elects to apply CC0 to the Work and publicly distribute the Work under its terms, with knowledge of his or her Copyright and Related Rights in the Work and the meaning and intended legal effect of CC0 on those rights.
14 |
15 | 1. __Copyright and Related Rights.__ A Work made available under CC0 may be protected by copyright and related or neighboring rights ("Copyright and Related Rights"). Copyright and Related Rights include, but are not limited to, the following:
16 |
17 | i. the right to reproduce, adapt, distribute, perform, display, communicate, and translate a Work;
18 |
19 | ii. moral rights retained by the original author(s) and/or performer(s);
20 |
21 | iii. publicity and privacy rights pertaining to a person's image or likeness depicted in a Work;
22 |
23 | iv. rights protecting against unfair competition in regards to a Work, subject to the limitations in paragraph 4(a), below;
24 |
25 | v. rights protecting the extraction, dissemination, use and reuse of data in a Work;
26 |
27 | vi. database rights (such as those arising under Directive 96/9/EC of the European Parliament and of the Council of 11 March 1996 on the legal protection of databases, and under any national implementation thereof, including any amended or successor version of such directive); and
28 |
29 | vii. other similar, equivalent or corresponding rights throughout the world based on applicable law or treaty, and any national implementations thereof.
30 |
31 | 2. __Waiver.__ To the greatest extent permitted by, but not in contravention of, applicable law, Affirmer hereby overtly, fully, permanently, irrevocably and unconditionally waives, abandons, and surrenders all of Affirmer's Copyright and Related Rights and associated claims and causes of action, whether now known or unknown (including existing as well as future claims and causes of action), in the Work (i) in all territories worldwide, (ii) for the maximum duration provided by applicable law or treaty (including future time extensions), (iii) in any current or future medium and for any number of copies, and (iv) for any purpose whatsoever, including without limitation commercial, advertising or promotional purposes (the "Waiver"). Affirmer makes the Waiver for the benefit of each member of the public at large and to the detriment of Affirmer's heirs and successors, fully intending that such Waiver shall not be subject to revocation, rescission, cancellation, termination, or any other legal or equitable action to disrupt the quiet enjoyment of the Work by the public as contemplated by Affirmer's express Statement of Purpose.
32 |
33 | 3. __Public License Fallback.__ Should any part of the Waiver for any reason be judged legally invalid or ineffective under applicable law, then the Waiver shall be preserved to the maximum extent permitted taking into account Affirmer's express Statement of Purpose. In addition, to the extent the Waiver is so judged Affirmer hereby grants to each affected person a royalty-free, non transferable, non sublicensable, non exclusive, irrevocable and unconditional license to exercise Affirmer's Copyright and Related Rights in the Work (i) in all territories worldwide, (ii) for the maximum duration provided by applicable law or treaty (including future time extensions), (iii) in any current or future medium and for any number of copies, and (iv) for any purpose whatsoever, including without limitation commercial, advertising or promotional purposes (the "License"). The License shall be deemed effective as of the date CC0 was applied by Affirmer to the Work. Should any part of the License for any reason be judged legally invalid or ineffective under applicable law, such partial invalidity or ineffectiveness shall not invalidate the remainder of the License, and in such case Affirmer hereby affirms that he or she will not (i) exercise any of his or her remaining Copyright and Related Rights in the Work or (ii) assert any associated claims and causes of action with respect to the Work, in either case contrary to Affirmer's express Statement of Purpose.
34 |
35 | 4. __Limitations and Disclaimers.__
36 |
37 | a. No trademark or patent rights held by Affirmer are waived, abandoned, surrendered, licensed or otherwise affected by this document.
38 |
39 | b. Affirmer offers the Work as-is and makes no representations or warranties of any kind concerning the Work, express, implied, statutory or otherwise, including without limitation warranties of title, merchantability, fitness for a particular purpose, non infringement, or the absence of latent or other defects, accuracy, or the present or absence of errors, whether or not discoverable, all to the greatest extent permissible under applicable law.
40 |
41 | c. Affirmer disclaims responsibility for clearing rights of other persons that may apply to the Work or any use thereof, including without limitation any person's Copyright and Related Rights in the Work. Further, Affirmer disclaims responsibility for obtaining any necessary consents, permissions or other rights required for any use of the Work.
42 |
43 | d. Affirmer understands and acknowledges that Creative Commons is not a party to this document and has no duty or obligation with respect to this CC0 or use of the Work.
44 |
--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
1 | # PubTator: tagged PubMed abstracts for literature mining
2 |
3 | [](https://travis-ci.org/greenelab/pubtator)
4 |
5 | [PubTator](https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/) and its 2.0 version ([PubTator Central](https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTatorCentral/)) uses text mining to tag PubMed abstracts/artciles with standardized concepts. This repository retrieves and processes PubTator annotations for use in [`greenelab/snorkeling`](https://github.com/greenelab/snorkeling) and elsewhere.
6 |
7 | # Get Started
8 |
9 | ## **Depreciation Notice**
10 |
11 | If you have arrived at this page in order to convert Pubtator into BioCXML format, you no longer need to.
12 | Pubtator Central now provides their own BioCXML files which can be found [here](https://ftp.ncbi.nlm.nih.gov/pub/lu/PubTatorCentral/PubTatorCentral_BioCXML/).
13 |
14 | ## Set-up Environment
15 |
16 | ### Conda
17 |
18 | 1. Install the [conda](https://conda.io) environment.
19 | 2. Create the pubtator environmenmt by running:
20 |
21 | ```sh
22 | conda create --name pubtator python=3.8
23 | ```
24 | 3. Install packages via pip by running the following:
25 |
26 | ```sh
27 | pip install -r requirements.txt
28 | ```
29 |
30 | 4. Activate with `conda activate pubtator`.
31 |
32 | ### Pip
33 |
34 | 1. Make sure you have python version **3.8** installed.
35 | 2. Install packages by running the following:
36 |
37 | ```sh
38 | pip install -r requirements.txt
39 | ```
40 |
41 |
42 | ## Execution
43 |
44 | To start processing Pubtator/Pubtator Central run the following command:
45 |
46 | ```sh
47 | python execute.py --config config_files/pubtator_central_config.json
48 | ```
49 |
50 | If the original Pubtator is desired replace `pubtator_central_config.json` with `pubtator_config.json`. The json file contains all the necessary parameters needed to run. More information for the json file can be found [here](config_files).
51 |
52 | ## License
53 |
54 | This repository is dual licensed as [BSD 3-Clause](LICENSE-BSD.md) and [CC0 1.0](LICENSE-CC0.md), meaning any repository content can be used under either license. This licensing arrangement ensures source code is available under an [OSI-approved License](https://opensource.org/licenses/alphabetical), while non-code content — such as figures, data, and documentation — is maximally reusable under a public domain dedication.
55 |
--------------------------------------------------------------------------------
/config_files/CONFIG.md:
--------------------------------------------------------------------------------
1 | # Configuration Files Explained
2 |
3 | This file explains the pipeline steps and parameters needed for each step.
4 | **Note: any added parameter or step will be ignored unless `execute.py` is manually changed.**
5 |
6 | ## Repository Download
7 |
8 | This is the first step of the Pubtator pipeline.
9 | Basically this step downloads Pubtator Central's annotation file from their ftp server.
10 |
11 | Following Parameters for this section:
12 | | Param | Description | Accepted Values |
13 | | --- | --- | --- |
14 | | url | the url to download the file from | a string with a url path |
15 | | download_folder | the folder to hold the downloaded file | a string name for the folder |
16 | | skip | tell execute.py to ignore this step and contine | true or false |
17 |
18 | ## Pubtator to XML
19 |
20 | This is the second step of the Pubtator pipeline.
21 | This step converts Pubtator/Pubtator Central's annotation file into xml format.
22 | **Note: This step may take awhile to complete**
23 |
24 | Following Parameters for this section:
25 | | Param | Description | Accepted Values |
26 | | --- | --- | --- |
27 | | documents | The file path pointing to the downloaded file from the previous step. | a string for the file path |
28 | | output | The file path to save the xml file. Make sure to keep the xz extension. | a string for the file path |
29 | | skip | Tell execute.py to ignore this step and contine | true or false |
30 |
31 | ## Extract Tags
32 |
33 | This is the second step of the Pubtator pipeline.
34 | This step extracts Pubtator/Pubtator Central's annotations from the xml file.
35 | It outputs a tsv file that contains all extracted annotation.
36 | **Note: This step may take awhile to complete**
37 |
38 | Following Parameters for this section:
39 | | Param | Description | Accepted Values |
40 | | --- | --- | --- |
41 | | input | The file path pointing to the xml file in previouss step. Make sure to keep the xz extension. | a string for the file path |
42 | | output | The file path to save the tsv file. Make sure to keep the xz extension. | a string for the file path |
43 | | skip | Tell execute.py to ignore this step and contine | true or false |
44 |
45 | ## Hetnet ID Extractor
46 |
47 | This is the third step of the Pubtator pipeline.
48 | This step filters out extracted annotations to only include tags within [Hetionet's Database](https://het.io/).
49 |
50 | Following Parameters for this section:
51 | | Param | Description | Accepted Values |
52 | | --- | --- | --- |
53 | | input | The file path pointing to the tsv file in previous step. Make sure to keep the xz extension. | a string for the file path |
54 | | output | The file path to save the tsv file. Make sure to keep the xz extension. | a string for the file path |
55 | | skip | Tell execute.py to ignore this step and contine | true or false |
56 |
57 | ## Map PMIDS to PMCIDS
58 |
59 | This is the forth step of the Pubtator pipeline.
60 | This step querys NCBI's pmid to pmcid mapper in order to grab PMCIDS.
61 | **Note: To download full text you will need to have PMCIDS. PMIDS will not work.**
62 |
63 | Following Parameters for this section:
64 | | Param | Description | Accepted Values |
65 | | --- | --- | --- |
66 | | input | The file path pointing to the tsv file in extract tags step. Make sure to keep the xz extension. | a string for the file path |
67 | | output | The file path to save the tsv file. | a string for the file path |
68 | | debug | This is a flag for debugging purposes. Feel free to ignore and leave as false. | true or false |
69 | | skip | Tell execute.py to ignore this step and contine | true or false |
70 |
71 | ## Download Full Text
72 |
73 | This is the fifth step of the Pubtator pipeline.
74 | This step queries Pubtator Central's api and downloads annotated full text if text is present.
75 |
76 | Following Parameters for this section:
77 | | Param | Description | Accepted Values |
78 | | --- | --- | --- |
79 | | input | The file path pointing to the tsv file in previous step. | a string for the file path |
80 | | output | The file path to save the xml file. | a string for the file path |
81 | | temp_dir | The folder to hold temporary batch files for this step of the pipeline | a string for the folder path |
82 | | log_file | A log file that keeps track of the IDs that have already been queried. It is used to monitor progress in case the process is interrupted. Make sure it has the tsv extension. | a file path for the file |
83 | | skip | Tell execute.py to ignore this step and contine | true or false |
84 |
85 | ## Extract Full Text Tags
86 |
87 | This is the sixth step of the Pubtator pipeline.
88 | This step extracts tags from full text documents.
89 | Please refer to [Extract Tags Section](#extract-tags) for parameter details.
90 |
91 | ## Hetnet ID Extractor Full Text
92 |
93 | This is the last step of the Pubtator pipeline.
94 | This step filters tags to only have Hetionet tags.
95 | Please refer to [Hetnet ID Extractor Section](#hetnet-id-extractor) for parameter details.
96 |
97 |
--------------------------------------------------------------------------------
/config_files/README.md:
--------------------------------------------------------------------------------
1 | # Configuration Files
2 |
3 | ## File Description
4 |
5 | | File | Description |
6 | | --- | --- |
7 | | [pubtator central config](pubtator_central_config.json) | This is a configuration file for parsing Pubtator Central. |
8 | | [pubtator config](pubtator_config.json) | This is a configuration file for parsing Pubtator (older version of Pubtator Central). |
9 | | [tests config](tests_config.json) | This is a configuration file for testing the pubtator system. Feel free to ignore this file. |
10 |
11 | ## Usage
12 |
13 | Each configuration file is in json format and contains parameters for each step within the pubtator pipeline.
14 | All files are organized by order of operation, which means the very first step occurs at the top and the subsequent step comes right afterwards.
15 | Every step can be skipped, which allows one to continue the pipeline at any step one chooses.
16 | Please refer to [CONFIG.md](CONFIG.md) for more details on each pipeline step and their respective parameters.
17 |
18 | Example config file:
19 | ```json
20 | {
21 | "pipeline step 1":{
22 | "param1":"param1_value",
23 | "param2":"param2_value",
24 | "skip":false
25 | },
26 | "pipeline step 2":{
27 | "param1":"param1_value",
28 | "param2":"param2_value",
29 | "skip":false
30 | },
31 | "pipeline step 3":{
32 | "param1":"param1_value",
33 | "param2":"param2_value",
34 | "skip":false
35 | }
36 | }
37 | ```
38 |
--------------------------------------------------------------------------------
/config_files/pubtator_central_config.json:
--------------------------------------------------------------------------------
1 | {
2 | "repository_download":{
3 | "url":"ftp://ftp.ncbi.nlm.nih.gov/pub/lu/PubTatorCentral/bioconcepts2pubtatorcentral.offset.gz",
4 | "download_folder":"download",
5 | "skip":false
6 | },
7 |
8 | "pubtator_to_xml": {
9 | "documents":"download/bioconcepts2pubtatorcentral.offset.gz",
10 | "output":"data/pubtator-central-docs.xml.xz",
11 | "skip":false
12 | },
13 |
14 | "extract_tags":{
15 | "input":"data/pubtator-central-docs.xml.xz",
16 | "output":"data/pubtator-central-tags.tsv.xz",
17 | "skip":false
18 | },
19 |
20 | "hetnet_id_extractor":{
21 | "input":"data/pubtator-central-tags.tsv.xz",
22 | "output":"data/pubtator-central-hetnet-tags.tsv.xz",
23 | "skip":false
24 | },
25 |
26 | "map_pmids_to_pmcids":{
27 | "input":"data/pubtator-central-tags.tsv.xz",
28 | "output":"data/pubtator-pmids-to-pmcids.tsv",
29 | "debug":false,
30 | "skip":false
31 | },
32 |
33 | "download_full_text":{
34 | "input":"data/pubtator-pmids-to-pmcids.tsv",
35 | "document_batch":100,
36 | "output":" data/pubtator-central-full-text.xml",
37 | "temp_dir":"data/temp",
38 | "log_file":"batch_log.tsv",
39 | "skip":false
40 | },
41 |
42 | "extract_full_text_tags":{
43 | "input":"data/pubtator-central-full-text.xml",
44 | "output":"data/pubtator-central-full-text-tags.tsv.xz",
45 | "skip":false
46 | },
47 |
48 | "hetnet_id_extractor_full_text":{
49 | "input":"data/pubtator-central-full-text-tags.tsv.xz",
50 | "output":"data/pubtator-central-full-hetnet-tags.tsv.xz",
51 | "skip":false
52 | }
53 |
54 | }
55 |
--------------------------------------------------------------------------------
/config_files/pubtator_config.json:
--------------------------------------------------------------------------------
1 | {
2 | "repository_download":{
3 | "url":"ftp://ftp.ncbi.nlm.nih.gov/pub/lu/PubTator/bioconcepts2pubtator_offsets.gz",
4 | "download_folder":"download",
5 | "skip":false
6 | },
7 |
8 | "pubtator_to_xml": {
9 | "documents":"download/bioconcepts2pubtator_offsets.gz",
10 | "output":"data/pubtator-docs.xml.xz",
11 | "skip":false
12 | },
13 |
14 | "extract_tags":{
15 | "input":"data/pubtator-docs.xml.xz",
16 | "output":"data/pubtator-tags.tsv.xz",
17 | "skip":false
18 | },
19 |
20 | "hetnet_id_extractor":{
21 | "input":"data/pubtator-tags.tsv.xz",
22 | "output":"data/pubtator-hetnet-tags.tsv.xz",
23 | "skip":false
24 | }
25 | }
26 |
--------------------------------------------------------------------------------
/config_files/tests_config.json:
--------------------------------------------------------------------------------
1 | {
2 | "repository_download":{
3 | "url":"ftp://ftp.ncbi.nlm.nih.gov/pub/lu/PubTatorCentral/bioconcepts2pubtatorcentral.offset.gz",
4 | "download_folder":"download",
5 | "skip":true
6 | },
7 |
8 | "pubtator_to_xml": {
9 | "documents":"data/example/1-sample-annotations.txt",
10 | "output":"data/example/2-sample-docs.xml",
11 | "skip":false
12 | },
13 |
14 | "extract_tags":{
15 | "input":"data/example/2-sample-docs.xml",
16 | "output":"data/example/3-sample-tags.tsv",
17 | "skip":false
18 | },
19 |
20 | "hetnet_id_extractor":{
21 | "input":"data/example/3-sample-tags.tsv",
22 | "output":"data/example/4-hetnet-tags.tsv",
23 | "skip":false
24 | },
25 |
26 | "map_pmids_to_pmcids":{
27 | "input":"data/example/3-sample-tags.tsv",
28 | "output":"data/example/5-sample-pmids-to-pmcids.tsv",
29 | "debug":true,
30 | "skip":false
31 | },
32 |
33 | "download_full_text":{
34 | "input":"data/example/5-sample-pmids-to-pmcids.tsv",
35 | "document_batch":100,
36 | "output":"data/example/6-sample-full-text.xml",
37 | "temp_dir":"data/temp",
38 | "log_file":"batch_log.tsv",
39 | "skip":false
40 | },
41 |
42 | "extract_full_text_tags":{
43 | "input":"data/example/6-sample-full-text.xml",
44 | "output":"data/example/7-sample-full-text-tags.tsv",
45 | "skip":false
46 | },
47 |
48 | "hetnet_id_extractor_full_text":{
49 | "input":"data/example/7-sample-full-text-tags.tsv",
50 | "output":"data/example/8-hetnet-full-text-tags.tsv",
51 | "skip":false
52 | }
53 |
54 | }
55 |
--------------------------------------------------------------------------------
/data/.gitattributes:
--------------------------------------------------------------------------------
1 | pubtator-hetnet-tags.tsv.xz filter=lfs diff=lfs merge=lfs -text
2 |
--------------------------------------------------------------------------------
/data/example/5-sample-pmids-to-pmcids.tsv:
--------------------------------------------------------------------------------
1 | Journal Title ISSN eISSN Year Volume Issue Page DOI PMCID PMID Manuscript Id Release Date
2 | J Cell Biol 0021-9525 1540-8140 1992 117.0 2 427 10.1083/jcb.117.2.427 PMC2289422 1560033 live
3 | J Cell Biol 0021-9525 1540-8140 1992 117.0 2 269 10.1083/jcb.117.2.269 PMC2289423 1313813 live
4 | J Cell Biol 0021-9525 1540-8140 1992 117.0 2 311 10.1083/jcb.117.2.311 PMC2289424 1560028 live
5 | J Cell Biol 0021-9525 1540-8140 1992 117.0 2 437 10.1083/jcb.117.2.437 PMC2289425 1373145 live
6 | J Cell Biol 0021-9525 1540-8140 1992 117.0 2 245 10.1083/jcb.117.2.245 PMC2289426 1560026 live
7 | J Cell Biol 0021-9525 1540-8140 1992 117.0 2 291 10.1083/jcb.117.2.291 PMC2289427 1313814 live
8 | J Cell Biol 0021-9525 1540-8140 1992 117.0 2 461 10.1083/jcb.117.2.461 PMC2289428 1560035 live
9 | J Cell Biol 0021-9525 1540-8140 1992 117.0 2 337 10.1083/jcb.117.2.337 PMC2289429 1373142 live
10 | J Cell Biol 0021-9525 1540-8140 1992 117.0 2 327 10.1083/jcb.117.2.327 PMC2289430 1560029 live
11 | J Cell Biol 0021-9525 1540-8140 1992 117.0 3 659 10.1083/jcb.117.3.659 PMC2289434 1374069 live
12 | J Cell Biol 0021-9525 1540-8140 1992 117.0 3 493 10.1083/jcb.117.3.493 PMC2289435 1315314 live
13 | J Cell Biol 0021-9525 1540-8140 1992 117.0 3 679 10.1083/jcb.117.3.679 PMC2289436 1572896 live
14 | J Cell Biol 0021-9525 1540-8140 1992 117.0 3 629 10.1083/jcb.117.3.629 PMC2289437 1315318 live
15 | J Cell Biol 0021-9525 1540-8140 1992 117.0 3 515 10.1083/jcb.117.3.515 PMC2289438 1572893 live
16 | J Cell Biol 0021-9525 1540-8140 1992 117.0 3 687 10.1083/jcb.117.3.687 PMC2289439 1572897 live
17 | J Cell Biol 0021-9525 1540-8140 1992 117.0 3 595 10.1083/jcb.117.3.595 PMC2289440 1533397 live
18 | J Cell Biol 0021-9525 1540-8140 1992 117.0 3 505 10.1083/jcb.117.3.505 PMC2289441 1315315 live
19 | J Cell Biol 0021-9525 1540-8140 1992 117.0 3 607 10.1083/jcb.117.3.607 PMC2289442 1374068 live
20 | J Cell Biol 0021-9525 1540-8140 1992 117.0 3 583 10.1083/jcb.117.3.583 PMC2289443 1374067 live
21 | J Cell Biol 0021-9525 1540-8140 1992 117.0 3 483 10.1083/jcb.117.3.483 PMC2289444 1374066 live
22 | J Cell Biol 0021-9525 1540-8140 1992 117.0 3 565 10.1083/jcb.117.3.565 PMC2289445 1315317 live
23 | J Cell Biol 0021-9525 1540-8140 1992 117.0 3 617 10.1083/jcb.117.3.617 PMC2289446 1349305 live
24 | J Cell Biol 0021-9525 1540-8140 1992 117.0 3 539 10.1083/jcb.117.3.539 PMC2289447 1572894 live
25 | J Cell Biol 0021-9525 1540-8140 1992 117.0 3 551 10.1083/jcb.117.3.551 PMC2289448 1572895 live
26 | J Cell Biol 0021-9525 1540-8140 1992 117.0 3 671 10.1083/jcb.117.3.671 PMC2289449 1533398 live
27 | J Cell Biol 0021-9525 1540-8140 1992 117.0 3 531 10.1083/jcb.117.3.531 PMC2289450 1315316 live
28 | J Cell Biol 0021-9525 1540-8140 1992 117.0 3 573 10.1083/jcb.117.3.573 PMC2289451 1533396 live
29 | J Cell Biol 0021-9525 1540-8140 1992 117.0 3 473 10.1083/jcb.117.3.473 PMC2289452 1572892 live
30 | J Cell Biol 0021-9525 1540-8140 1992 117.0 3 643 10.1083/jcb.117.3.643 PMC2289453 1315319 live
31 | J Cell Biol 0021-9525 1540-8140 1992 117.0 4 895 10.1083/jcb.117.4.895 PMC2289454 1374413 live
32 | J Cell Biol 0021-9525 1540-8140 1992 117.0 4 863 10.1083/jcb.117.4.863 PMC2289455 1577862 live
33 | J Cell Biol 0021-9525 1540-8140 1992 117.0 4 745 10.1083/jcb.117.4.745 PMC2289456 1577854 live
34 | J Cell Biol 0021-9525 1540-8140 1992 117.0 4 729 10.1083/jcb.117.4.729 PMC2289457 1577853 live
35 | J Cell Biol 0021-9525 1540-8140 1992 117.0 4 757 10.1083/jcb.117.4.757 PMC2289458 1577855 live
36 | J Cell Biol 0021-9525 1540-8140 1992 117.0 4 717 10.1083/jcb.117.4.717 PMC2289459 1577852 live
37 | J Cell Biol 0021-9525 1540-8140 1992 117.0 4 849 10.1083/jcb.117.4.849 PMC2289460 1577861 live
38 | J Cell Biol 0021-9525 1540-8140 1992 117.0 4 787 10.1083/jcb.117.4.787 PMC2289461 1577858 live
39 | J Cell Biol 0021-9525 1540-8140 1992 117.0 4 825 10.1083/jcb.117.4.825 PMC2289462 1349609 live
40 | J Cell Biol 0021-9525 1540-8140 1992 117.0 4 775 10.1083/jcb.117.4.775 PMC2289463 1577857 live
41 | J Cell Biol 0021-9525 1540-8140 1992 117.0 4 889 10.1083/jcb.117.4.889 PMC2289464 1315783 live
42 | J Cell Biol 0021-9525 1540-8140 1992 117.0 4 841 10.1083/jcb.117.4.841 PMC2289465 1577860 live
43 | J Cell Biol 0021-9525 1540-8140 1992 117.0 4 765 10.1083/jcb.117.4.765 PMC2289466 1577856 live
44 | J Cell Biol 0021-9525 1540-8140 1992 117.0 4 903 10.1083/jcb.117.4.903 PMC2289467 1577863 live
45 | J Cell Biol 0021-9525 1540-8140 1992 117.0 4 813 10.1083/jcb.117.4.813 PMC2289468 1349608 live
46 | J Cell Biol 0021-9525 1540-8140 1992 117.0 4 701 10.1083/jcb.117.4.701 PMC2289469 1577851 live
47 | J Cell Biol 0021-9525 1540-8140 1992 117.0 4 799 10.1083/jcb.117.4.799 PMC2289470 1577859 live
48 | J Cell Biol 0021-9525 1540-8140 1992 117.0 4 877 10.1083/jcb.117.4.877 PMC2289471 1315782 live
49 | J Cell Biol 0021-9525 1540-8140 1992 117.0 5 1109 10.1083/jcb.117.5.1109 PMC2289472 1374416 live
50 | J Cell Biol 0021-9525 1540-8140 1992 117.0 5 1085 10.1083/jcb.117.5.1085 PMC2289473 1577867 live
51 | J Cell Biol 0021-9525 1540-8140 1992 117.0 5 1119 10.1083/jcb.117.5.1119 PMC2289474 1577869 live
52 | J Cell Biol 0021-9525 1540-8140 1992 117.0 5 1067 10.1083/jcb.117.5.1067 PMC2289475 1315784 live
53 | J Cell Biol 0021-9525 1540-8140 1992 117.0 5 1041 10.1083/jcb.117.5.1041 PMC2289476 1533642 live
54 | J Cell Biol 0021-9525 1540-8140 1992 117.0 5 1023 10.1083/jcb.117.5.1023 PMC2289477 1577865 live
55 | J Cell Biol 0021-9525 1540-8140 1992 117.0 5 987 10.1083/jcb.117.5.987 PMC2289478 1315787 live
56 | J Cell Biol 0021-9525 1540-8140 1992 117.0 5 935 10.1083/jcb.117.5.935 PMC2289479 1315786 live
57 | J Cell Biol 0021-9525 1540-8140 1992 117.0 5 1055 10.1083/jcb.117.5.1055 PMC2289480 1533643 live
58 | J Cell Biol 0021-9525 1540-8140 1992 117.0 5 1077 10.1083/jcb.117.5.1077 PMC2289481 1374414 live
59 | J Cell Biol 0021-9525 1540-8140 1992 117.0 5 1093 10.1083/jcb.117.5.1093 PMC2289482 1577868 live
60 | J Cell Biol 0021-9525 1540-8140 1992 117.0 5 1031 10.1083/jcb.117.5.1031 PMC2289483 1577866 live
61 | J Cell Biol 0021-9525 1540-8140 1992 117.0 5 1007 10.1083/jcb.117.5.1007 PMC2289484 1577864 live
62 | J Cell Biol 0021-9525 1540-8140 1992 117.0 5 921 10.1083/jcb.117.5.921 PMC2289485 1315785 live
63 | J Cell Biol 0021-9525 1540-8140 1992 117.0 5 959 10.1083/jcb.117.5.959 PMC2289486 1374417 live
64 | J Cell Biol 0021-9525 1540-8140 1992 117.0 5 975 10.1083/jcb.117.5.975 PMC2289487 1577871 live
65 | J Cell Biol 0021-9525 1540-8140 1992 117.0 5 949 10.1083/jcb.117.5.949 PMC2289488 1577870 live
66 | J Cell Biol 0021-9525 1540-8140 1992 117.0 5 1101 10.1083/jcb.117.5.1101 PMC2289489 1374415 live
67 | J Cell Biol 0021-9525 1540-8140 1992 117.0 5 997 10.1083/jcb.117.5.997 PMC2289490 1577872 live
68 | J Cell Biol 0021-9525 1540-8140 1992 117.0 6 1223 10.1083/jcb.117.6.1223 PMC2289491 1607384 live
69 | J Cell Biol 0021-9525 1540-8140 1992 117.0 6 1181 10.1083/jcb.117.6.1181 PMC2289492 1607382 live
70 | J Cell Biol 0021-9525 1540-8140 1992 117.0 6 1251 10.1083/jcb.117.6.1251 PMC2289493 1607387 live
71 | J Cell Biol 0021-9525 1540-8140 1992 117.0 6 1197 10.1083/jcb.117.6.1197 PMC2289494 1318883 live
72 | J Cell Biol 0021-9525 1540-8140 1992 117.0 6 1137 10.1083/jcb.117.6.1137 PMC2289495 1607378 live
73 | J Cell Biol 0021-9525 1540-8140 1992 117.0 6 1321 10.1083/jcb.117.6.1321 PMC2289496 1376731 live
74 | J Cell Biol 0021-9525 1540-8140 1992 117.0 6 1277 10.1083/jcb.117.6.1277 PMC2289497 1607389 live
75 | J Cell Biol 0021-9525 1540-8140 1992 117.0 6 1161 10.1083/jcb.117.6.1161 PMC2289498 1607380 live
76 | J Cell Biol 0021-9525 1540-8140 1992 117.0 6 1231 10.1083/jcb.117.6.1231 PMC2289499 1607385 live
77 | J Cell Biol 0021-9525 1540-8140 1992 117.0 6 1211 10.1083/jcb.117.6.1211 PMC2289500 1607383 live
78 | J Cell Biol 0021-9525 1540-8140 1992 117.0 6 1351 10.1083/jcb.117.6.1351 PMC2289501 1607393 live
79 | J Cell Biol 0021-9525 1540-8140 1992 117.0 6 1151 10.1083/jcb.117.6.1151 PMC2289502 1607379 live
80 | J Cell Biol 0021-9525 1540-8140 1992 117.0 6 1331 10.1083/jcb.117.6.1331 PMC2289503 1607392 live
81 | J Cell Biol 0021-9525 1540-8140 1992 117.0 6 1171 10.1083/jcb.117.6.1171 PMC2289504 1607381 live
82 | J Cell Biol 0021-9525 1540-8140 1992 117.0 6 1311 10.1083/jcb.117.6.1311 PMC2289505 1607391 live
83 | J Cell Biol 0021-9525 1540-8140 1992 117.0 6 1299 10.1083/jcb.117.6.1299 PMC2289506 1318884 live
84 | J Cell Biol 0021-9525 1540-8140 1992 117.0 6 1263 10.1083/jcb.117.6.1263 PMC2289507 1607388 live
85 | J Cell Biol 0021-9525 1540-8140 1992 117.0 6 1343 10.1083/jcb.117.6.1343 PMC2289508 1376732 live
86 | J Cell Biol 0021-9525 1540-8140 1992 117.0 6 1241 10.1083/jcb.117.6.1241 PMC2289509 1607386 live
87 | J Cell Biol 0021-9525 1540-8140 1992 117.0 6 1289 10.1083/jcb.117.6.1289 PMC2289510 1607390 live
88 | J Cell Biol 0021-9525 1540-8140 1992 118.0 1 51 10.1083/jcb.118.1.51 PMC2289512 1352300 live
89 | J Cell Biol 0021-9525 1540-8140 1992 118.0 1 43 10.1083/jcb.118.1.43 PMC2289513 1320035 live
90 | J Cell Biol 0021-9525 1540-8140 1992 118.0 1 203 10.1083/jcb.118.1.203 PMC2289514 1618904 live
91 | J Cell Biol 0021-9525 1540-8140 1992 118.0 1 1 10.1083/jcb.118.1.1 PMC2289515 1618896 live
92 | J Cell Biol 0021-9525 1540-8140 1992 118.0 1 177 10.1083/jcb.118.1.177 PMC2289517 1618903 live
93 | J Cell Biol 0021-9525 1540-8140 1992 118.0 1 23 10.1083/jcb.118.1.23 PMC2289518 1618905 live
94 | J Cell Biol 0021-9525 1540-8140 1992 118.0 1 163 10.1083/jcb.118.1.163 PMC2289519 1618902 live
95 | J Cell Biol 0021-9525 1540-8140 1992 118.0 1 95 10.1083/jcb.118.1.95 PMC2289520 1618910 live
96 | J Cell Biol 0021-9525 1540-8140 1992 118.0 1 11 10.1083/jcb.118.1.11 PMC2289521 1618898 live
97 | J Cell Biol 0021-9525 1540-8140 1992 118.0 1 33 10.1083/jcb.118.1.33 PMC2289522 1618906 live
98 | J Cell Biol 0021-9525 1540-8140 1992 118.0 1 131 10.1083/jcb.118.1.131 PMC2289524 1618900 live
99 | J Cell Biol 0021-9525 1540-8140 1992 118.0 1 71 10.1083/jcb.118.1.71 PMC2289525 1618908 live
100 | Acta Neuropathol Commun 2051-5960 2014 2 176 10.1186/s40478-014-0176-9 PMC4272812 25497491 live
101 | BMC Med Educ 1472-6920 2014 14 258 10.1186/s12909-014-0258-1 PMC4272813 25491129 live
102 | Gut Pathog 1757-4749 2014 6 46 10.1186/s13099-014-0046-9 PMC4272814 25530808 live
103 | Clin Epigenetics 1868-7075 1868-7083 2014 6 1 32 10.1186/s13148-014-0032-6 PMC4272815 25530820 live
104 | Aquat Toxicol 0166-445X 1879-1514 2014 0 192 10.1016/j.aquatox.2014.11.016 PMC4272816 25481785 NIHMS645550 live
105 | BMC Med Educ 1472-6920 2014 14 263 10.1186/s12909-014-0263-4 PMC4272818 25495467 live
106 | Prehosp Emerg Care 1090-3127 1545-0066 2014 18 3 368 10.3109/10903127.2013.869642 PMC4272820 24548058 NIHMS644369 live
107 | Skelet Muscle 2044-5040 2014 4 23 10.1186/s13395-014-0023-5 PMC4272821 25530839 live
108 | BMC Genet 1471-2156 2014 15 144 10.1186/s12863-014-0144-1 PMC4272822 25511509 live
109 | Radiat Oncol 1748-717X 2014 9 277 10.1186/s13014-014-0277-4 PMC4272823 25497602 live
110 | Drug Alcohol Depend 0376-8716 1879-0046 2014 0 52 10.1016/j.drugalcdep.2014.11.003 PMC4272824 25439054 NIHMS643973 live
111 | Sci Transl Med 1946-6234 1946-6242 2014 6 246 246ra96 10.1126/scitranslmed.3008680 PMC4272825 25101886 NIHMS623565 live
112 | Blood Cells Mol Dis 1079-9796 1096-0961 2013 52 1 68 10.1016/j.bcmd.2013.07.003 PMC4272826 23910958 NIHMS648290 live
113 | Mater Sociomed 1512-7680 1986-597X 2014 26 5 329 10.5455/msm.2014.26.329-334 PMC4272827 25568633 live
114 | Mater Sociomed 1512-7680 1986-597X 2014 26 5 303 10.5455/msm.2014.26.303-305 PMC4272828 25568626 live
115 | Mater Sociomed 1512-7680 1986-597X 2014 26 5 306 10.5455/msm.2014.26.306-308 PMC4272829 25568627 live
116 | Mater Sociomed 1512-7680 1986-597X 2014 26 5 335 10.5455/msm.2014.26.335-338 PMC4272830 25568634 live
117 | Mater Sociomed 1512-7680 1986-597X 2014 26 5 297 10.5455/msm.2014.26.297-302 PMC4272831 25568625 live
118 | Acta Inform Med 0353-8109 1986-5988 2014 22 5 329 10.5455/aim.2014.22.329-332 PMC4272832 25568583 live
119 | Acta Inform Med 0353-8109 1986-5988 2014 22 5 302 10.5455/aim.2014.22.302-305 PMC4272833 25568577 live
120 | Mater Sociomed 1512-7680 1986-597X 2014 26 5 292 10.5455/msm.2014.26.292-296 PMC4272834 25568624 live
121 | Acta Inform Med 0353-8109 1986-5988 2014 22 5 292 10.5455/aim.2014.22.292-296 PMC4272835 25568575 live
122 | Mater Sociomed 1512-7680 1986-597X 2014 26 5 309 10.5455/msm.2014.26.309-312 PMC4272836 25568628 live
123 | Acta Inform Med 0353-8109 1986-5988 2014 22 5 341 10.5455/aim.2014.22.341-346 PMC4272837 25568585 live
124 | Mater Sociomed 1512-7680 1986-597X 2014 26 5 343 10.5455/msm.2014.26.343-347 PMC4272838 25568636 live
125 | Acta Inform Med 0353-8109 1986-5988 2014 22 5 333 10.5455/aim.2014.22.333-340 PMC4272839 25568584 live
126 | Mater Sociomed 1512-7680 1986-597X 2014 26 5 348 10.5455/msm.2014.26.348-351 PMC4272840 25568637 live
127 | Acta Inform Med 0353-8109 1986-5988 2014 22 5 350 10.5455/aim.2014.22.350-350 PMC4272841 25568587 live
128 | Mater Sociomed 1512-7680 1986-597X 2014 26 5 321 10.5455/msm.2014.26.321-323 PMC4272842 25568631 live
129 | Acta Inform Med 0353-8109 1986-5988 2014 22 5 325 10.5455/aim.2014.22.325-328 PMC4272843 25568582 live
130 | Acta Inform Med 0353-8109 1986-5988 2014 22 5 347 10.5455/aim.2014.22.347-349 PMC4272844 25568586 live
131 | Mater Sociomed 1512-7680 1986-597X 2014 26 5 318 10.5455/msm.2014.26.318-320 PMC4272845 25568630 live
132 | Acta Inform Med 0353-8109 1986-5988 2014 22 5 297 10.5455/aim.2014.22.297-301 PMC4272846 25568576 live
133 | Acta Inform Med 0353-8109 1986-5988 2014 22 5 315 10.5455/aim.2014.22.315-319 PMC4272847 25568580 live
134 |
--------------------------------------------------------------------------------
/data/example/8-hetnet-full-text-tags.tsv:
--------------------------------------------------------------------------------
1 | pubmed_id type identifier offset end
2 | 2289422 Compound DB00126 514 527
3 | 2289422 Compound DB09541 514 527
4 | 2289422 Compound DB00755 1544 1557
5 | 2289423 Compound DB00134 524 534
6 | 2289423 Compound DB00134 606 616
7 | 2289423 Compound DB00065 1042 1046
8 | 2289423 Compound DB00065 1224 1228
9 | 2289423 Compound DB00065 1331 1337
10 | 2289423 Compound DB00065 1523 1529
11 | 2289423 Compound DB00065 1569 1575
12 | 2289423 Compound DB00065 2016 2020
13 | 2289424 Compound DB00145 590 597
14 | 2289424 Compound DB00135 598 606
15 | 2289424 Compound DB00135 1143 1151
16 | 2289424 Compound DB00145 1155 1162
17 | 2289424 Compound DB00145 1679 1686
18 | 2289424 Compound DB00135 1687 1695
19 | 2289425 Gene 7531 297 301
20 | 2289427 Gene 1877 543 546
21 | 2289428 Gene 838 634 667
22 | 2289428 Gene 496 681 691
23 | 2289428 Gene 3054 1095 1101
24 | 2289428 Gene 3054 1417 1423
25 | 2289429 Compound DB00065 26 30
26 | 2289429 Disease DOID:2531 450 457
27 | 2289429 Compound DB00065 570 574
28 | 2289429 Compound DB00065 1541 1545
29 | 2289429 Compound DB00065 1630 1634
30 | 2289430 Compound DB03193 994 1006
31 | 2289434 Gene 3054 63 69
32 | 2289434 Gene 3054 471 477
33 | 2289434 Gene 3054 517 523
34 | 2289434 Gene 3054 611 617
35 | 2289434 Gene 3054 713 719
36 | 2289434 Gene 838 821 827
37 | 2289434 Gene 838 933 939
38 | 2289434 Gene 3054 1008 1014
39 | 2289434 Gene 3054 1029 1035
40 | 2289434 Gene 22999 1075 1090
41 | 2289434 Disease DOID:1909 1237 1245
42 | 2289434 Gene 3054 1401 1407
43 | 2289434 Gene 3054 1419 1425
44 | 2289434 Gene 3054 1591 1597
45 | 2289434 Gene 3054 1790 1796
46 | 2289434 Gene 22999 2082 2097
47 | 2289434 Gene 3054 2157 2163
48 | 2289434 Gene 3054 2240 2246
49 | 2289436 Gene 540 0 31
50 | 2289436 Gene 540 449 480
51 | 2289436 Gene 540 482 490
52 | 2289436 Gene 540 1563 1571
53 | 2289437 Gene 1876 14 38
54 | 2289437 Gene 1876 130 154
55 | 2289437 Gene 1876 156 159
56 | 2289437 Compound DB00624 205 217
57 | 2289437 Gene 1876 386 389
58 | 2289437 Gene 1876 488 491
59 | 2289437 Gene 1877 627 639
60 | 2289437 Gene 1877 712 724
61 | 2289437 Gene 1877 833 845
62 | 2289437 Gene 1876 1004 1007
63 | 2289437 Gene 1876 1204 1207
64 | 2289440 Gene 55829 281 300
65 | 2289440 Gene 55829 302 305
66 | 2289440 Gene 55829 416 419
67 | 2289440 Gene 55829 496 499
68 | 2289440 Gene 55829 660 663
69 | 2289440 Gene 55829 859 862
70 | 2289440 Gene 1545 907 913
71 | 2289440 Gene 1545 1255 1261
72 | 2289440 Gene 55829 1439 1442
73 | 2289440 Gene 1545 1512 1518
74 | 2289440 Gene 55829 1648 1651
75 | 2289440 Gene 1545 1671 1678
76 | 2289441 Compound DB09152 264 265
77 | 2289441 Gene 3908 889 892
78 | 2289443 Gene 55643 62 75
79 | 2289443 Gene 55643 278 281
80 | 2289443 Gene 55643 361 364
81 | 2289443 Gene 55643 585 588
82 | 2289443 Gene 55643 769 772
83 | 2289443 Gene 55643 857 860
84 | 2289443 Gene 55643 906 909
85 | 2289443 Gene 55643 1175 1178
86 | 2289445 Gene 8829 95 121
87 | 2289445 Compound DB00065 210 214
88 | 2289445 Gene 8829 293 345
89 | 2289445 Gene 8829 406 409
90 | 2289445 Gene 8829 527 530
91 | 2289445 Gene 8829 1041 1044
92 | 2289445 Gene 539 1180 1185
93 | 2289445 Gene 8829 1438 1441
94 | 2289446 Gene 4580 999 1004
95 | 2289447 Compound DB00171 603 606
96 | 2289447 Compound DB00640 603 606
97 | 2289447 Gene 2591 820 836
98 | 2289449 Disease DOID:219 259 279
99 | 2289449 Compound DB00974 852 856
100 | 2289449 Compound DB09153 870 874
101 | 2289449 Gene 22999 957 972
102 | 2289449 Gene 22999 1079 1094
103 | 2289449 Gene 22999 1176 1191
104 | 2289450 Gene 4502 58 99
105 | 2289450 Gene 4502 101 104
106 | 2289450 Gene 4502 201 204
107 | 2289450 Gene 4502 433 436
108 | 2289450 Gene 4502 527 530
109 | 2289450 Compound DB00171 1073 1076
110 | 2289450 Compound DB00640 1073 1076
111 | 2289450 Gene 4502 1185 1188
112 | 2289451 Compound DB00171 1235 1238
113 | 2289451 Compound DB00640 1235 1238
114 | 2289452 Compound DB00171 823 826
115 | 2289452 Compound DB00640 823 826
116 | 2289452 Compound DB00171 861 864
117 | 2289452 Compound DB00640 861 864
118 | 2289452 Compound DB00171 975 978
119 | 2289452 Compound DB00640 975 978
120 | 2289453 Compound DB00151 647 656
121 | 2289453 Compound DB09485 647 656
122 | 2289453 Compound DB00928 1553 1564
123 | 2289453 Gene 1850 1586 1590
124 | 2289453 Gene 22999 1685 1700
125 | 2289454 Compound DB00316 108 109
126 | 2289454 Gene 539 432 442
127 | 2289454 Gene 539 444 473
128 | 2289454 Gene 539 475 482
129 | 2289454 Gene 389 486 496
130 | 2289454 Gene 389 498 539
131 | 2289454 Gene 389 541 547
132 | 2289454 Gene 2260 555 565
133 | 2289454 Gene 2260 567 574
134 | 2289454 Gene 539 759 769
135 | 2289454 Gene 539 1061 1072
136 | 2289454 Gene 539 1286 1296
137 | 2289457 Gene 173 49 56
138 | 2289457 Gene 173 216 223
139 | 2289457 Compound DB09341 235 242
140 | 2289457 Compound DB11280 235 242
141 | 2289457 Gene 173 254 261
142 | 2289457 Compound DB09341 272 279
143 | 2289457 Compound DB11280 272 279
144 | 2289457 Gene 173 500 507
145 | 2289457 Compound DB09341 649 656
146 | 2289457 Compound DB11280 649 656
147 | 2289462 Compound DB00541 1918 1929
148 | 2289465 Gene 3908 0 3
149 | 2289465 Gene 3908 168 198
150 | 2289465 Gene 3908 200 203
151 | 2289465 Gene 3908 416 419
152 | 2289465 Gene 3908 571 574
153 | 2289465 Gene 3908 871 874
154 | 2289465 Gene 3908 892 895
155 | 2289465 Gene 3908 1046 1049
156 | 2289465 Gene 3908 1254 1257
157 | 2289465 Gene 3908 1331 1334
158 | 2289470 Compound DB00065 86 90
159 | 2289470 Compound DB00065 130 134
160 | 2289470 Compound DB00065 207 211
161 | 2289470 Compound DB00065 477 481
162 | 2289470 Compound DB00065 755 759
163 | 2289470 Compound DB00065 893 897
164 | 2289470 Compound DB00065 941 945
165 | 2289470 Compound DB00065 1006 1010
166 | 2289470 Compound DB00065 1208 1212
167 | 2289470 Compound DB00065 1238 1242
168 | 2289470 Compound DB00065 1368 1372
169 | 2289470 Compound DB00065 1404 1408
170 | 2289470 Compound DB00065 1448 1452
171 | 2289470 Compound DB00065 1501 1505
172 | 2289470 Compound DB00065 1574 1580
173 | 2289470 Compound DB00065 1630 1636
174 | 2289470 Compound DB00065 1673 1677
175 | 2289472 Compound DB00065 136 140
176 | 2289472 Compound DB00065 218 222
177 | 2289472 Compound DB00065 399 403
178 | 2289472 Compound DB00065 665 669
179 | 2289472 Compound DB00065 831 835
180 | 2289472 Compound DB00065 1162 1166
181 | 2289473 Gene 1876 184 203
182 | 2289473 Gene 1876 205 208
183 | 2289473 Gene 1876 559 562
184 | 2289473 Gene 1876 785 788
185 | 2289473 Gene 1876 835 838
186 | 2289473 Gene 4487 1059 1063
187 | 2289473 Gene 2538 1068 1076
188 | 2289474 Disease DOID:2994 424 443
189 | 2289474 Compound DB00974 630 634
190 | 2289474 Compound DB00974 1133 1137
191 | 2289480 Compound DB00171 1241 1244
192 | 2289480 Compound DB00640 1241 1244
193 | 2289484 Gene 7594 4 12
194 | 2289484 Gene 55553 24 37
195 | 2289484 Gene 7594 1101 1109
196 | 2289484 Gene 55553 1139 1152
197 | 2289484 Gene 55553 1156 1169
198 | 2289484 Gene 55553 1323 1336
199 | 2289484 Gene 55553 1474 1487
200 | 2289489 Gene 3772 757 767
201 | 2289489 Gene 3772 926 936
202 | 2289490 Gene 7594 720 728
203 | 2289490 Gene 7594 1457 1465
204 | 2289491 Gene 23480 44 50
205 | 2289491 Gene 23480 250 256
206 | 2289491 Gene 23480 335 341
207 | 2289491 Gene 23480 379 385
208 | 2289491 Gene 23480 468 474
209 | 2289491 Gene 23480 588 594
210 | 2289491 Gene 23480 651 657
211 | 2289491 Gene 23480 772 778
212 | 2289491 Gene 23480 893 899
213 | 2289491 Gene 23480 985 991
214 | 2289491 Gene 23480 1109 1115
215 | 2289491 Compound DB00171 1152 1155
216 | 2289491 Compound DB00640 1152 1155
217 | 2289491 Compound DB00171 1271 1276
218 | 2289491 Compound DB00640 1271 1276
219 | 2289491 Gene 23480 1306 1312
220 | 2289491 Gene 23480 1362 1368
221 | 2289491 Compound DB00171 1398 1403
222 | 2289491 Compound DB00640 1398 1403
223 | 2289491 Gene 23480 1455 1461
224 | 2289491 Gene 23480 1646 1652
225 | 2289491 Gene 23480 1698 1704
226 | 2289492 Compound DB00171 116 119
227 | 2289492 Compound DB00640 116 119
228 | 2289492 Gene 173 120 127
229 | 2289492 Gene 173 192 199
230 | 2289492 Gene 173 589 596
231 | 2289492 Gene 173 832 839
232 | 2289492 Gene 173 911 918
233 | 2289492 Disease DOID:1826 1006 1024
234 | 2289492 Gene 173 1070 1077
235 | 2289492 Gene 173 1161 1168
236 | 2289492 Compound DB00171 1217 1220
237 | 2289492 Compound DB00640 1217 1220
238 | 2289492 Compound DB00171 1296 1299
239 | 2289492 Compound DB00640 1296 1299
240 | 2289492 Compound DB00171 1385 1388
241 | 2289492 Compound DB00640 1385 1388
242 | 2289492 Gene 173 1465 1472
243 | 2289492 Compound DB00171 1529 1532
244 | 2289492 Compound DB00640 1529 1532
245 | 2289492 Gene 173 1594 1616
246 | 2289492 Compound DB00171 1691 1694
247 | 2289492 Compound DB00640 1691 1694
248 | 2289492 Gene 173 1709 1716
249 | 2289492 Compound DB09353 1755 1756
250 | 2289492 Gene 173 1868 1890
251 | 2289492 Gene 173 2034 2041
252 | 2289492 Compound DB00171 2117 2120
253 | 2289492 Compound DB00640 2117 2120
254 | 2289492 Gene 173 2134 2141
255 | 2289492 Disease DOID:1826 2369 2387
256 | 2289495 Compound DB00171 838 841
257 | 2289495 Compound DB00640 838 841
258 | 2289495 Compound DB00171 1582 1585
259 | 2289495 Compound DB00640 1582 1585
260 | 2289496 Gene 22999 46 61
261 | 2289496 Gene 22999 149 164
262 | 2289496 Compound DB00172 1561 1568
263 | 2289496 Compound DB00172 1709 1716
264 | 2289496 Compound DB00133 1859 1865
265 | 2289496 Compound DB00135 1870 1878
266 | 2289498 Gene 328 59 63
267 | 2289498 Gene 328 414 418
268 | 2289498 Gene 328 560 564
269 | 2289498 Gene 328 776 780
270 | 2289498 Gene 328 982 986
271 | 2289498 Gene 328 1033 1037
272 | 2289498 Gene 328 1501 1505
273 | 2289498 Gene 328 1652 1656
274 | 2289498 Gene 328 1907 1911
275 | 2289499 Compound DB00171 464 467
276 | 2289499 Compound DB00640 464 467
277 | 2289499 Compound DB09407 662 667
278 | 2289499 Compound DB09407 937 942
279 | 2289499 Compound DB00171 1067 1070
280 | 2289499 Compound DB00640 1067 1070
281 | 2289500 Compound DB00608 966 977
282 | 2289500 Compound DB00608 1102 1113
283 | 2289501 Disease DOID:12365 0 19
284 | 2289501 Compound DB01109 574 581
285 | 2289501 Disease DOID:12365 1114 1131
286 | 2289501 Compound DB00686 1160 1180
287 | 2289501 Compound DB01109 1186 1193
288 | 2289501 Compound DB01109 1581 1588
289 | 2289503 Disease DOID:1909 88 96
290 | 2289503 Gene 2253 214 218
291 | 2289503 Disease DOID:1909 242 250
292 | 2289503 Disease DOID:1909 405 413
293 | 2289503 Compound DB01109 466 473
294 | 2289503 Disease DOID:1909 500 508
295 | 2289503 Disease DOID:1909 711 719
296 | 2289503 Gene 2253 725 729
297 | 2289503 Gene 2253 838 842
298 | 2289503 Gene 2253 995 999
299 | 2289503 Gene 2253 1107 1111
300 | 2289503 Disease DOID:1909 1132 1140
301 | 2289503 Gene 2253 1204 1208
302 | 2289503 Gene 2253 1325 1329
303 | 2289503 Gene 2253 1391 1395
304 | 2289503 Gene 2253 1587 1591
305 | 2289503 Disease DOID:1909 1635 1648
306 | 2289503 Disease DOID:1909 1740 1748
307 | 2289503 Gene 2253 1762 1766
308 | 2289503 Gene 2253 1844 1848
309 | 2289503 Gene 2253 1869 1873
310 | 2289503 Disease DOID:1909 1908 1916
311 | 2289503 Gene 2253 1950 1954
312 | 2289503 Compound DB09153 2020 2024
313 | 2289503 Gene 2253 2081 2085
314 | 2289503 Gene 2253 2140 2144
315 | 2289503 Gene 2253 2247 2251
316 | 2289503 Disease DOID:1909 2261 2269
317 | 2289503 Disease DOID:1909 2393 2401
318 | 2289504 Compound DB09353 1795 1796
319 | 2289505 Disease DOID:1192 66 79
320 | 2289505 Disease DOID:1192 176 189
321 | 2289505 Compound DB01394 624 634
322 | 2289506 Gene 3856 53 63
323 | 2289506 Gene 3856 314 324
324 | 2289506 Gene 3856 326 330
325 | 2289506 Gene 3856 386 390
326 | 2289506 Gene 9670 424 428
327 | 2289506 Gene 3856 556 560
328 | 2289506 Gene 3856 636 640
329 | 2289506 Gene 3856 689 693
330 | 2289506 Gene 3856 857 861
331 | 2289506 Gene 3856 1081 1085
332 | 2289506 Gene 3856 1545 1549
333 | 2289506 Gene 3856 1835 1839
334 | 2289507 Gene 55829 34 53
335 | 2289507 Gene 55829 291 310
336 | 2289507 Gene 55829 500 519
337 | 2289507 Gene 55829 562 581
338 | 2289507 Gene 55829 878 897
339 | 2289507 Gene 55829 1109 1128
340 | 2289507 Compound DB01229 1331 1336
341 | 2289507 Gene 55829 1419 1438
342 | 2289508 Gene 55890 435 440
343 | 2289508 Gene 55890 493 498
344 | 2289508 Gene 55890 645 650
345 | 2289508 Compound DB08818 753 763
346 | 2289509 Gene 23480 403 409
347 | 2289509 Gene 23480 669 675
348 | 2289509 Compound DB00171 713 716
349 | 2289509 Compound DB00640 713 716
350 | 2289509 Gene 23480 980 986
351 | 2289509 Gene 23480 1057 1063
352 | 2289510 Compound DB01394 126 136
353 | 2289510 Compound DB01394 315 325
354 | 2289510 Compound DB01394 1651 1661
355 | 2289510 Compound DB01394 1913 1923
356 | 2289510 Compound DB01394 2282 2292
357 | 2289510 Compound DB01394 2390 2400
358 | 2289514 Disease DOID:2355 607 618
359 | 2289515 Compound DB00171 928 931
360 | 2289515 Compound DB00640 928 931
361 | 2289517 Compound DB00065 1949 1953
362 | 2289524 Gene 1876 0 19
363 | 2289524 Gene 1876 643 662
364 | 2289524 Gene 1876 664 667
365 | 2289524 Gene 1876 719 722
366 | 2289524 Gene 1876 873 876
367 | 2289525 Gene 23480 1683 1689
368 | 2289525 Gene 23480 1931 1937
369 | 4272812 Gene 293 10 25
370 | 4272812 Disease DOID:14330 41 60
371 | 4272812 Disease DOID:14330 61 80
372 | 4272812 Disease DOID:14330 82 84
373 | 4272812 Gene 293 303 318
374 | 4272812 Gene 293 320 329
375 | 4272812 Gene 293 446 455
376 | 4272812 Disease DOID:14330 495 497
377 | 4272812 Disease DOID:14330 557 559
378 | 4272812 Gene 293 765 774
379 | 4272812 Gene 293 817 826
380 | 4272812 Gene 293 1051 1060
381 | 4272812 Gene 55937 1069 1074
382 | 4272812 Gene 293 1203 1212
383 | 4272812 Compound DB00988 1334 1342
384 | 4272812 Compound DB00988 1344 1346
385 | 4272812 Gene 293 1377 1386
386 | 4272812 Disease DOID:14330 1495 1497
387 | 4272812 Disease DOID:14330 1604 1623
388 | 4272812 Disease DOID:14330 1625 1627
389 | 4272812 Disease DOID:14330 1854 1856
390 | 4272812 Disease DOID:2377 1862 1880
391 | 4272812 Disease DOID:14330 2071 2073
392 | 4272812 Disease DOID:14330 2199 2201
393 | 4272812 Disease DOID:14330 2530 2532
394 | 4272812 Disease DOID:14330 2683 2685
395 | 4272812 Disease DOID:1319 3924 3936
396 | 4272812 Disease DOID:1319 4111 4123
397 | 4272812 Disease DOID:14330 4473 4475
398 | 4272812 Disease DOID:14330 4915 4917
399 | 4272812 Disease DOID:10652 5011 5030
400 | 4272812 Disease DOID:14330 5036 5047
401 | 4272812 Gene 293 6252 6261
402 | 4272812 Gene 293 6790 6799
403 | 4272812 Gene 293 7067 7076
404 | 4272812 Gene 293 7162 7171
405 | 4272812 Gene 293 7219 7228
406 | 4272812 Gene 8534 7480 7518
407 | 4272812 Gene 8534 7520 7526
408 | 4272812 Gene 8534 7748 7754
409 | 4272812 Disease DOID:10652 8359 8378
410 | 4272812 Disease DOID:14330 9978 9980
411 | 4272812 Gene 293 10499 10508
412 | 4272812 Gene 55937 10599 10604
413 | 4272812 Disease DOID:14330 11206 11208
414 | 4272812 Disease DOID:14330 11225 11227
415 | 4272812 Disease DOID:14330 11445 11447
416 | 4272812 Gene 293 11470 11479
417 | 4272812 Disease DOID:14330 11530 11532
418 | 4272812 Disease DOID:14330 11638 11640
419 | 4272812 Gene 293 11661 11670
420 | 4272812 Gene 293 12094 12103
421 | 4272812 Disease DOID:14330 12493 12495
422 | 4272812 Disease DOID:14330 12550 12552
423 | 4272812 Disease DOID:14330 12667 12669
424 | 4272812 Disease DOID:14330 12941 12943
425 | 4272812 Disease DOID:14330 13140 13142
426 | 4272812 Disease DOID:14330 13232 13243
427 | 4272812 Gene 293 13535 13544
428 | 4272812 Gene 293 13546 13550
429 | 4272812 Gene 293 13704 13708
430 | 4272812 Gene 293 13843 13852
431 | 4272812 Gene 293 13854 13858
432 | 4272812 Disease DOID:14330 13985 13987
433 | 4272812 Gene 293 14040 14044
434 | 4272812 Disease DOID:14330 14089 14091
435 | 4272812 Gene 293 14192 14196
436 | 4272812 Disease DOID:14330 14268 14270
437 | 4272812 Gene 293 14410 14414
438 | 4272812 Disease DOID:14330 14475 14477
439 | 4272812 Gene 293 14797 14801
440 | 4272812 Disease DOID:14330 14879 14881
441 | 4272812 Disease DOID:14330 14981 14983
442 | 4272812 Gene 293 14994 14998
443 | 4272812 Gene 293 15071 15080
444 | 4272812 Gene 293 15382 15386
445 | 4272812 Gene 293 15448 15457
446 | 4272812 Gene 293 15556 15560
447 | 4272812 Disease DOID:14330 15683 15685
448 | 4272812 Gene 293 15984 15988
449 | 4272812 Disease DOID:14330 16084 16086
450 | 4272812 Gene 293 16106 16110
451 | 4272812 Disease DOID:14330 16251 16253
452 | 4272812 Disease DOID:14330 16436 16438
453 | 4272812 Disease DOID:14330 16540 16542
454 | 4272812 Disease DOID:14330 16604 16606
455 | 4272812 Disease DOID:14330 16660 16662
456 | 4272812 Disease DOID:14330 16731 16761
457 | 4272812 Disease DOID:14330 16783 16785
458 | 4272812 Disease DOID:14330 18531 18533
459 | 4272812 Disease DOID:14330 18667 18669
460 | 4272812 Gene 293 18935 18944
461 | 4272812 Disease DOID:14330 19100 19111
462 | 4272812 Disease DOID:14330 19145 19147
463 | 4272812 Disease DOID:14330 19264 19266
464 | 4272812 Gene 293 20236 20251
465 | 4272812 Disease DOID:14330 20697 20699
466 | 4272812 Compound DB00988 20843 20851
467 | 4272812 Compound DB01235 20843 20851
468 | 4272812 Disease DOID:14330 20863 20865
469 | 4272812 Disease DOID:14330 21011 21013
470 | 4272812 Gene 293 21179 21188
471 | 4272812 Disease DOID:14330 22419 22421
472 | 4272812 Compound DB00988 22536 22544
473 | 4272812 Disease DOID:14330 22775 22777
474 | 4272812 Disease DOID:14330 22991 22993
475 | 4272812 Gene 293 23064 23073
476 | 4272812 Disease DOID:14330 23155 23157
477 | 4272812 Disease DOID:14330 23528 23530
478 | 4272812 Disease DOID:14330 24663 24665
479 | 4272812 Gene 293 24883 24887
480 | 4272812 Disease DOID:14330 25202 25204
481 | 4272812 Gene 55937 25307 25312
482 | 4272812 Gene 293 25352 25361
483 | 4272812 Disease DOID:14330 25436 25438
484 | 4272812 Gene 293 25634 25643
485 | 4272812 Gene 55937 25703 25708
486 | 4272812 Disease DOID:14330 26093 26095
487 | 4272812 Disease DOID:14330 26266 26268
488 | 4272812 Gene 293 26558 26567
489 | 4272812 Gene 293 27052 27061
490 | 4272812 Gene 293 27175 27184
491 | 4272812 Compound DB01032 27270 27280
492 | 4272812 Gene 293 27419 27428
493 | 4272812 Gene 293 27765 27774
494 | 4272812 Gene 293 27962 27971
495 | 4272812 Compound DB01032 28135 28145
496 | 4272812 Disease DOID:14330 28521 28523
497 | 4272812 Gene 293 28825 28834
498 | 4272812 Disease DOID:14330 28924 28926
499 | 4272812 Gene 293 28947 28956
500 | 4272812 Gene 293 29199 29208
501 | 4272812 Gene 293 29296 29305
502 | 4272812 Gene 293 29581 29590
503 | 4272812 Disease DOID:14330 29788 29790
504 | 4272812 Disease DOID:14330 30105 30107
505 | 4272812 Gene 293 30194 30203
506 | 4272812 Disease DOID:14330 30845 30847
507 | 4272812 Gene 293 31103 31112
508 | 4272812 Gene 293 31566 31575
509 | 4272812 Disease DOID:14330 31661 31663
510 | 4272812 Disease DOID:14330 31780 31782
511 | 4272812 Gene 293 31977 31986
512 | 4272812 Gene 293 32563 32572
513 | 4272812 Gene 293 32675 32684
514 | 4272812 Gene 293 32731 32740
515 | 4272812 Gene 293 32855 32864
516 | 4272812 Gene 293 32912 32921
517 | 4272812 Disease DOID:14330 33006 33008
518 | 4272812 Gene 293 33050 33059
519 | 4272812 Gene 307 33369 33389
520 | 4272812 Gene 293 33555 33564
521 | 4272812 Disease DOID:14330 33632 33634
522 | 4272812 Gene 293 33759 33768
523 | 4272812 Gene 293 34299 34308
524 | 4272812 Disease DOID:14330 34614 34616
525 | 4272812 Gene 293 34842 34851
526 | 4272812 Gene 293 35104 35113
527 | 4272812 Gene 293 35247 35256
528 | 4272812 Disease DOID:14330 35453 35455
529 | 4272812 Disease DOID:14330 35877 35879
530 | 4272812 Gene 293 36090 36099
531 | 4272812 Gene 293 36120 36129
532 | 4272812 Gene 293 36298 36307
533 | 4272812 Gene 293 36820 36829
534 | 4272812 Disease DOID:14330 36834 36836
535 | 4272812 Gene 5182 36887 36891
536 | 4272812 Gene 293 37011 37020
537 | 4272812 Gene 293 37075 37084
538 | 4272812 Gene 5182 37190 37194
539 | 4272812 Gene 293 37277 37286
540 | 4272812 Gene 293 37365 37374
541 | 4272812 Gene 55937 37476 37481
542 | 4272812 Gene 433 37493 37497
543 | 4272812 Disease DOID:14330 37714 37716
544 | 4272812 Gene 433 37748 37752
545 | 4272812 Gene 433 37838 37857
546 | 4272812 Gene 433 37897 37901
547 | 4272812 Gene 293 37927 37936
548 | 4272812 Gene 433 37987 37991
549 | 4272812 Gene 293 38005 38014
550 | 4272812 Gene 293 38040 38049
551 | 4272812 Gene 293 38161 38170
552 | 4272812 Gene 433 38237 38241
553 | 4272812 Gene 540 38267 38276
554 | 4272812 Disease DOID:14330 38351 38353
555 | 4272812 Gene 540 38412 38421
556 | 4272812 Disease DOID:14330 38514 38516
557 | 4272812 Gene 540 38535 38544
558 | 4272812 Gene 540 38758 38767
559 | 4272812 Gene 55937 38870 38875
560 | 4272812 Gene 540 38929 38938
561 | 4272812 Disease DOID:14330 39006 39008
562 | 4272812 Compound DB00988 39131 39133
563 | 4272812 Gene 55937 39268 39273
564 | 4272812 Gene 293 39310 39319
565 | 4272812 Gene 293 39439 39448
566 | 4272812 Gene 293 39633 39642
567 | 4272812 Gene 293 39811 39820
568 | 4272812 Gene 293 39886 39895
569 | 4272812 Gene 293 40044 40053
570 | 4272812 Gene 293 40228 40237
571 | 4272812 Disease DOID:14330 40373 40375
572 | 4272812 Disease DOID:14330 40553 40555
573 | 4272812 Disease DOID:14330 40644 40646
574 | 4272812 Gene 293 40717 40726
575 | 4272812 Gene 293 40820 40829
576 | 4272812 Gene 293 40950 40954
577 | 4272812 Disease DOID:14330 41063 41065
578 | 4272812 Gene 293 41115 41124
579 | 4272812 Disease DOID:14330 41185 41187
580 | 4272812 Gene 55937 41209 41214
581 | 4272812 Gene 293 41235 41244
582 | 4272812 Gene 55937 41299 41304
583 | 4272812 Gene 55937 41354 41359
584 | 4272812 Gene 55937 41549 41554
585 | 4272812 Gene 55937 41889 41894
586 | 4272812 Disease DOID:14330 41990 41992
587 | 4272812 Gene 293 42054 42063
588 | 4272812 Disease DOID:14330 42218 42220
589 | 4272812 Gene 293 42685 42694
590 | 4272812 Disease DOID:14330 43099 43101
591 | 4272812 Compound DB00988 43188 43196
592 | 4272812 Gene 293 43248 43257
593 | 4272812 Compound DB00988 43267 43269
594 | 4272812 Gene 293 43328 43337
595 | 4272812 Gene 307 43347 43367
596 | 4272812 Compound DB00988 43478 43484
597 | 4272812 Compound DB01235 43478 43484
598 | 4272812 Compound DB00988 43488 43490
599 | 4272812 Compound DB00988 43516 43518
600 | 4272812 Gene 293 43572 43581
601 | 4272812 Gene 55937 43587 43592
602 | 4272812 Gene 293 43649 43658
603 | 4272812 Gene 55937 43686 43691
604 | 4272812 Gene 293 43710 43719
605 | 4272812 Gene 293 43906 43915
606 | 4272812 Compound DB00988 43984 43986
607 | 4272812 Gene 55547 44104 44107
608 | 4272812 Compound DB00988 44381 44383
609 | 4272812 Compound DB00988 44435 44437
610 | 4272812 Compound DB00988 44484 44486
611 | 4272812 Gene 293 44506 44515
612 | 4272812 Disease DOID:14330 44809 44811
613 | 4272812 Gene 293 44838 44847
614 | 4272812 Gene 55937 44900 44905
615 | 4272812 Compound DB00988 45004 45006
616 | 4272812 Gene 293 45040 45055
617 | 4272812 Compound DB00988 45081 45083
618 | 4272812 Gene 293 45099 45108
619 | 4272812 Disease DOID:14330 45181 45183
620 | 4272812 Disease DOID:14330 45259 45261
621 | 4272812 Gene 293 45413 45422
622 | 4272812 Gene 293 45493 45502
623 | 4272812 Gene 293 45587 45596
624 | 4272812 Gene 293 45722 45731
625 | 4272812 Gene 293 45785 45794
626 | 4272812 Gene 293 45842 45851
627 | 4272812 Gene 293 46074 46083
628 | 4272812 Gene 293 46129 46138
629 | 4272812 Gene 293 46226 46235
630 | 4272812 Gene 293 46313 46322
631 | 4272812 Compound DB00988 46334 46336
632 | 4272812 Gene 293 46394 46403
633 | 4272812 Compound DB00988 46408 46410
634 | 4272812 Gene 293 46436 46445
635 | 4272812 Gene 293 46651 46660
636 | 4272812 Gene 293 46696 46705
637 | 4272812 Gene 293 46922 46931
638 | 4272812 Gene 293 47212 47221
639 | 4272812 Gene 293 47525 47534
640 | 4272812 Gene 293 47862 47871
641 | 4272812 Gene 293 47920 47929
642 | 4272812 Gene 293 48027 48036
643 | 4272812 Compound DB00172 48351 48358
644 | 4272812 Gene 293 48442 48451
645 | 4272812 Gene 55937 48963 48968
646 | 4272812 Gene 55937 49068 49073
647 | 4272812 Gene 55937 49126 49131
648 | 4272812 Gene 293 49288 49297
649 | 4272812 Gene 293 49373 49382
650 | 4272812 Gene 293 49447 49456
651 | 4272812 Gene 293 49785 49794
652 | 4272812 Gene 293 50773 50782
653 | 4272812 Gene 293 50888 50892
654 | 4272812 Gene 293 50981 50990
655 | 4272812 Gene 293 51149 51158
656 | 4272812 Gene 293 51355 51364
657 | 4272812 Gene 293 51433 51442
658 | 4272812 Gene 293 51632 51641
659 | 4272812 Gene 293 51702 51711
660 | 4272812 Gene 293 52074 52078
661 | 4272812 Disease DOID:14330 52087 52089
662 | 4272812 Gene 293 52149 52158
663 | 4272812 Gene 293 52364 52373
664 | 4272812 Compound DB00133 52517 52523
665 | 4272812 Gene 293 52540 52549
666 | 4272812 Compound DB00133 52650 52656
667 | 4272812 Gene 293 52729 52738
668 | 4272812 Gene 293 52821 52830
669 | 4272812 Gene 293 52898 52907
670 | 4272812 Gene 293 53323 53332
671 | 4272812 Gene 293 53397 53406
672 | 4272812 Disease DOID:14330 53421 53432
673 | 4272812 Gene 293 53592 53601
674 | 4272812 Gene 293 53779 53788
675 | 4272812 Gene 293 53991 54000
676 | 4272812 Gene 293 54125 54134
677 | 4272812 Disease DOID:14330 54158 54160
678 | 4272812 Gene 293 54267 54276
679 | 4272812 Gene 55937 54294 54299
680 | 4272812 Compound DB00988 54466 54474
681 | 4272812 Disease DOID:14330 54541 54543
682 | 4272812 Disease DOID:14330 54544 54563
683 | 4272812 Disease DOID:14330 54717 54736
684 | 4272812 Disease DOID:14330 54795 54812
685 | 4272812 Disease DOID:14330 54834 54853
686 | 4272812 Gene 293 54929 54944
687 | 4272812 Disease DOID:14330 54978 54997
688 | 4272812 Compound DB00988 55028 55036
689 | 4272812 Disease DOID:14330 55052 55071
690 | 4272812 Disease DOID:14330 55096 55115
691 | 4272812 Disease DOID:14330 55183 55213
692 | 4272812 Disease DOID:10652 55309 55341
693 | 4272812 Disease DOID:14330 55354 55371
694 | 4272812 Disease DOID:14330 55496 55515
695 | 4272812 Disease DOID:14330 55592 55611
696 | 4272812 Disease DOID:14330 55626 55663
697 | 4272812 Gene 293 55666 55681
698 | 4272812 Gene 293 55941 55956
699 | 4272812 Gene 293 56010 56025
700 | 4272812 Disease DOID:14330 56150 56169
701 | 4272812 Gene 293 56277 56281
702 | 4272812 Gene 293 56282 56297
703 | 4272812 Disease DOID:14330 56354 56373
704 | 4272812 Gene 293 56603 56618
705 | 4272812 Gene 293 56634 56649
706 | 4272812 Disease DOID:14330 56885 56902
707 | 4272812 Gene 8534 57066 57072
708 | 4272812 Gene 293 57398 57413
709 | 4272812 Disease DOID:14330 57469 57488
710 | 4272812 Disease DOID:14330 57547 57566
711 | 4272812 Gene 293 57584 57599
712 | 4272812 Disease DOID:14330 57699 57718
713 | 4272812 Disease DOID:14330 57765 57784
714 | 4272812 Disease DOID:14330 57841 57860
715 | 4272812 Disease DOID:14330 57933 57952
716 | 4272812 Disease DOID:14330 57955 57998
717 | 4272812 Disease DOID:14330 58031 58074
718 | 4272812 Disease DOID:14330 58100 58117
719 | 4272812 Disease DOID:14330 58164 58192
720 | 4272812 Disease DOID:14330 58358 58377
721 | 4272812 Gene 293 58380 58395
722 | 4272812 Disease DOID:14330 58422 58441
723 | 4272812 Disease DOID:14330 58496 58528
724 | 4272812 Gene 293 58654 58669
725 | 4272812 Disease DOID:14330 58673 58692
726 | 4272812 Gene 293 58722 58737
727 | 4272812 Disease DOID:14330 58778 58797
728 | 4272812 Gene 293 58854 58869
729 | 4272812 Gene 293 58903 58918
730 | 4272812 Gene 293 58951 58966
731 | 4272812 Disease DOID:14330 59007 59024
732 | 4272812 Gene 293 59181 59185
733 | 4272812 Disease DOID:14330 59191 59219
734 | 4272812 Disease DOID:14330 59236 59264
735 | 4272812 Gene 293 59295 59310
736 | 4272812 Disease DOID:14330 59341 59358
737 | 4272812 Gene 293 59410 59425
738 | 4272812 Gene 293 59427 59431
739 | 4272812 Disease DOID:14330 59459 59478
740 | 4272812 Gene 293 59481 59496
741 | 4272812 Disease DOID:14330 59533 59552
742 | 4272812 Gene 293 59555 59570
743 | 4272812 Disease DOID:14330 59604 59623
744 | 4272812 Gene 293 59698 59713
745 | 4272812 Disease DOID:14330 59821 59840
746 | 4272812 Disease DOID:14330 59856 59882
747 | 4272812 Gene 293 59903 59918
748 | 4272812 Gene 293 60019 60034
749 | 4272812 Gene 293 60168 60183
750 | 4272812 Gene 293 60327 60342
751 | 4272812 Compound DB00988 60394 60402
752 | 4272812 Gene 293 60493 60508
753 | 4272812 Gene 293 60631 60635
754 | 4272812 Disease DOID:14330 60683 60700
755 | 4272812 Disease DOID:14330 60763 60782
756 | 4272812 Disease DOID:14330 60883 60902
757 | 4272812 Disease DOID:14330 60959 60978
758 | 4272812 Disease DOID:14330 61034 61051
759 | 4272812 Disease DOID:14330 61118 61135
760 | 4272812 Disease DOID:14330 61210 61229
761 | 4272812 Gene 293 61457 61472
762 | 4272812 Gene 293 61506 61521
763 | 4272812 Disease DOID:14330 61563 61595
764 | 4272812 Disease DOID:14330 61659 61688
765 | 4272812 Disease DOID:14330 61796 61829
766 | 4272812 Gene 293 61895 61910
767 | 4272812 Gene 293 61921 61936
768 | 4272812 Disease DOID:14330 62027 62044
769 | 4272812 Disease DOID:14330 62104 62121
770 | 4272812 Disease DOID:14330 62341 62360
771 | 4272812 Disease DOID:14330 62419 62438
772 | 4272812 Disease DOID:14330 62725 62744
773 | 4272812 Disease DOID:14330 62832 62851
774 | 4272812 Compound DB00988 62856 62862
775 | 4272812 Compound DB01235 62856 62862
776 | 4272812 Disease DOID:14330 62954 62973
777 | 4272812 Gene 293 63093 63108
778 | 4272812 Gene 293 63278 63293
779 | 4272812 Disease DOID:14330 63406 63425
780 | 4272812 Disease DOID:14330 63449 63468
781 | 4272812 Disease DOID:14330 63658 63677
782 | 4272812 Compound DB01577 63834 63849
783 | 4272812 Gene 293 63911 63926
784 | 4272812 Disease DOID:14330 63971 63990
785 | 4272812 Disease DOID:14330 64002 64004
786 | 4272812 Compound DB01032 64283 64293
787 | 4272812 Gene 293 64409 64424
788 | 4272812 Disease DOID:14330 64499 64518
789 | 4272812 Disease DOID:14330 64565 64584
790 | 4272812 Disease DOID:14330 64659 64678
791 | 4272812 Disease DOID:14330 64740 64759
792 | 4272812 Gene 293 64847 64862
793 | 4272812 Gene 293 64940 64955
794 | 4272812 Gene 293 65117 65132
795 | 4272812 Gene 293 65201 65216
796 | 4272812 Disease DOID:14330 65256 65275
797 | 4272812 Disease DOID:14330 65315 65366
798 | 4272812 Disease DOID:14330 65406 65425
799 | 4272812 Disease DOID:14330 65506 65525
800 | 4272812 Disease DOID:14330 65795 65814
801 | 4272812 Disease DOID:14330 66149 66168
802 | 4272812 Disease DOID:14330 66268 66285
803 | 4272812 Disease DOID:14330 66315 66334
804 | 4272812 Disease DOID:14330 66417 66434
805 | 4272812 Disease DOID:14330 66495 66514
806 | 4272812 Compound DB00988 66583 66591
807 | 4272812 Gene 293 66608 66623
808 | 4272812 Disease DOID:14330 66669 66688
809 | 4272812 Disease DOID:14330 66718 66737
810 | 4272812 Gene 293 66753 66768
811 | 4272812 Disease DOID:14330 66925 66944
812 | 4272812 Gene 293 66980 66995
813 | 4272812 Gene 293 67141 67156
814 | 4272812 Disease DOID:14330 67178 67197
815 | 4272812 Gene 293 67198 67213
816 | 4272812 Gene 293 67510 67525
817 | 4272812 Disease DOID:14330 67814 67833
818 | 4272812 Disease DOID:14330 68110 68129
819 | 4272812 Gene 293 68147 68162
820 | 4272812 Disease DOID:14330 68210 68229
821 | 4272812 Gene 293 68263 68278
822 | 4272812 Gene 5182 68444 68448
823 | 4272812 Compound DB00988 68485 68493
824 | 4272812 Gene 293 68507 68522
825 | 4272812 Gene 293 68532 68547
826 | 4272812 Gene 4509 68575 68580
827 | 4272812 Gene 433 68590 68594
828 | 4272812 Compound DB00988 68615 68623
829 | 4272812 Gene 433 68632 68636
830 | 4272812 Gene 293 68677 68692
831 | 4272812 Disease DOID:14330 68702 68721
832 | 4272812 Gene 433 68754 68758
833 | 4272812 Disease DOID:14330 68820 68839
834 | 4272812 Gene 540 68842 68875
835 | 4272812 Disease DOID:14330 68954 68973
836 | 4272812 Gene 540 68976 68986
837 | 4272812 Disease DOID:14330 69033 69052
838 | 4272812 Gene 540 69090 69123
839 | 4272812 Gene 540 69254 69264
840 | 4272812 Gene 540 69359 69369
841 | 4272812 Compound DB00988 69383 69391
842 | 4272812 Gene 293 69396 69411
843 | 4272812 Gene 55937 69427 69432
844 | 4272812 Disease DOID:14330 69534 69553
845 | 4272812 Gene 293 69564 69579
846 | 4272812 Gene 293 69661 69676
847 | 4272812 Gene 55937 69762 69767
848 | 4272812 Disease DOID:14330 69901 69920
849 | 4272812 Gene 293 69923 69938
850 | 4272812 Disease DOID:14330 69975 69994
851 | 4272812 Gene 293 70053 70068
852 | 4272812 Compound DB00988 70076 70084
853 | 4272812 Gene 293 70299 70314
854 | 4272812 Gene 293 70358 70373
855 | 4272812 Gene 307 70399 70419
856 | 4272812 Gene 293 70443 70458
857 | 4272812 Gene 307 70504 70524
858 | 4272812 Gene 293 70563 70578
859 | 4272812 Compound DB00988 70666 70674
860 | 4272812 Gene 293 70714 70729
861 | 4272812 Compound DB00988 70884 70892
862 | 4272812 Compound DB00988 71115 71123
863 | 4272812 Gene 293 71209 71224
864 | 4272812 Compound DB00988 71274 71282
865 | 4272812 Gene 293 71477 71492
866 | 4272812 Compound DB00988 71539 71547
867 | 4272812 Compound DB00988 71576 71584
868 | 4272812 Gene 293 71599 71614
869 | 4272812 Disease DOID:14330 71837 71856
870 | 4272812 Gene 293 71872 71887
871 | 4272812 Disease DOID:14330 71911 71943
872 | 4272812 Gene 293 71976 71991
873 | 4272812 Gene 293 72103 72118
874 | 4272812 Gene 293 72131 72146
875 | 4272812 Gene 293 72224 72239
876 | 4272812 Gene 293 72321 72336
877 | 4272812 Gene 293 72398 72413
878 | 4272812 Compound DB00988 72470 72478
879 | 4272812 Gene 293 72519 72534
880 | 4272812 Gene 293 72611 72626
881 | 4272812 Gene 293 72647 72662
882 | 4272812 Gene 293 72752 72767
883 | 4272812 Disease DOID:14330 72826 72845
884 | 4272812 Gene 293 72847 72862
885 | 4272812 Gene 293 72885 72900
886 | 4272812 Disease DOID:14330 72979 72998
887 | 4272812 Gene 293 73083 73098
888 | 4272812 Disease DOID:14330 73131 73150
889 | 4272812 Gene 293 73227 73242
890 | 4272812 Gene 293 73344 73359
891 | 4272812 Gene 293 73495 73510
892 | 4272812 Gene 293 73564 73579
893 | 4272812 Gene 293 73636 73651
894 | 4272812 Gene 293 73704 73719
895 | 4272812 Gene 293 73844 73859
896 | 4272812 Compound DB00988 73877 73885
897 | 4272812 Gene 293 73886 73901
898 | 4272812 Compound DB00988 73909 73917
899 | 4272812 Compound DB00988 73922 73928
900 | 4272812 Compound DB01235 73922 73928
901 | 4272812 Disease DOID:14330 73976 73987
902 | 4272812 Disease DOID:10652 73992 74011
903 | 4272812 Gene 293 74039 74054
904 | 4272812 Disease DOID:14330 74134 74162
905 | 4272812 Gene 293 74343 74358
906 | 4272812 Disease DOID:14330 74391 74410
907 | 4272812 Compound DB00133 74442 74445
908 | 4272812 Gene 293 74459 74474
909 | 4272812 Disease DOID:14330 74522 74539
910 | 4272812 Disease DOID:14330 74666 74685
911 | 4272812 Gene 293 74743 74758
912 | 4272812 Gene 293 75024 75039
913 | 4272813 Disease DOID:10763 8551 8563
914 | 4272814 Compound DB00172 172 179
915 | 4272814 Compound DB00172 1443 1450
916 | 4272814 Compound DB06756 1455 1470
917 | 4272814 Compound DB00149 6340 6347
918 | 4272814 Compound DB00167 6348 6358
919 | 4272814 Compound DB09341 7806 7813
920 | 4272814 Compound DB11280 7806 7813
921 | 4272814 Compound DB00125 7821 7829
922 | 4272814 Compound DB00167 7837 7847
923 | 4272814 Compound DB00161 7855 7861
924 | 4272814 Compound DB09153 8118 8122
925 | 4272814 Compound DB00172 10539 10546
926 | 4272814 Compound DB09153 10584 10588
927 | 4272814 Compound DB09153 10837 10841
928 | 4272814 Compound DB00172 10926 10933
929 | 4272814 Compound DB09153 10961 10965
930 | 4272814 Compound DB09153 11167 11171
931 | 4272814 Compound DB09153 11305 11309
932 | 4272814 Compound DB09153 11332 11336
933 | 4272814 Compound DB09153 11690 11694
934 | 4272814 Compound DB09153 11847 11851
935 | 4272814 Compound DB09153 13006 13010
936 | 4272814 Compound DB09153 13116 13120
937 | 4272814 Compound DB09153 13355 13359
938 | 4272814 Compound DB09153 13527 13531
939 | 4272814 Compound DB00172 15754 15761
940 | 4272814 Compound DB09153 16186 16190
941 | 4272814 Compound DB09153 16262 16266
942 | 4272814 Compound DB09153 17944 17948
943 | 4272814 Compound DB09153 18860 18864
944 | 4272814 Disease DOID:2531 19260 19262
945 | 4272814 Disease DOID:2531 19360 19362
946 | 4272814 Compound DB00172 19678 19685
947 | 4272814 Compound DB00583 20252 20261
948 | 4272814 Compound DB06756 20603 20618
949 | 4272815 Gene 208 39 43
950 | 4272815 Gene 208 419 433
951 | 4272815 Gene 208 435 439
952 | 4272815 Gene 208 513 517
953 | 4272815 Gene 208 1362 1366
954 | 4272815 Gene 208 3555 3559
955 | 4272815 Gene 210 3564 3568
956 | 4272815 Gene 208 3592 3596
957 | 4272815 Gene 208 3945 3949
958 | 4272815 Gene 208 3995 3999
959 | 4272815 Gene 208 5240 5244
960 | 4272815 Gene 3908 6982 6987
961 | 4272815 Compound DB00118 7304 7324
962 | 4272815 Compound DB09153 7438 7442
963 | 4272815 Compound DB00974 7467 7471
964 | 4272815 Compound DB03255 7497 7503
965 | 4272815 Compound DB00898 7527 7534
966 | 4272815 Gene 208 8557 8561
967 | 4272815 Gene 208 8580 8584
968 | 4272815 Gene 3908 9704 9709
969 | 4272815 Gene 3908 9804 9809
970 | 4272815 Gene 3908 9965 9970
971 | 4272815 Gene 208 10047 10051
972 | 4272815 Gene 208 10591 10595
973 | 4272815 Gene 3908 11045 11050
974 | 4272815 Gene 3908 12858 12863
975 | 4272815 Gene 208 13101 13105
976 | 4272815 Gene 3908 13245 13250
977 | 4272815 Gene 208 13399 13403
978 | 4272815 Gene 208 13552 13556
979 | 4272815 Gene 208 13595 13599
980 | 4272815 Gene 208 13982 13986
981 | 4272815 Gene 208 16816 16820
982 | 4272815 Gene 208 16937 16941
983 | 4272815 Gene 208 17978 17982
984 | 4272815 Gene 208 18502 18506
985 | 4272815 Gene 208 18601 18605
986 | 4272815 Gene 80218 20601 20606
987 | 4272815 Disease DOID:10283 21495 21510
988 | 4272816 Compound DB09140 2791 2797
989 | 4272816 Compound DB01390 7472 7490
990 | 4272816 Compound DB09153 12535 12539
991 | 4272818 Gene 4359 10741 10744
992 | 4272818 Gene 4359 10759 10762
993 | 4272818 Gene 4257 18215 18223
994 | 4272820 Disease DOID:1826 94 112
995 | 4272820 Compound DB00829 290 298
996 | 4272820 Compound DB00186 300 309
997 | 4272820 Compound DB00683 315 324
998 | 4272820 Compound DB00829 458 466
999 | 4272820 Compound DB00186 468 477
1000 | 4272820 Compound DB00683 483 492
1001 | 4272820 Compound DB00829 1182 1190
1002 | 4272820 Compound DB00683 1221 1230
1003 | 4272820 Compound DB00186 1256 1265
1004 | 4272820 Compound DB00186 1521 1530
1005 | 4272820 Compound DB00683 1540 1549
1006 | 4272820 Compound DB00829 1553 1561
1007 | 4272820 Compound DB00683 1586 1595
1008 | 4272820 Compound DB00829 1600 1608
1009 | 4272820 Compound DB00186 1706 1715
1010 | 4272820 Disease DOID:1826 1883 1901
1011 | 4272820 Compound DB00683 2014 2023
1012 | 4272820 Disease DOID:1826 2063 2070
1013 | 4272820 Compound DB00829 2356 2364
1014 | 4272820 Compound DB00186 2369 2378
1015 | 4272820 Compound DB00683 2428 2437
1016 | 4272820 Compound DB00829 2630 2638
1017 | 4272820 Compound DB00186 2640 2649
1018 | 4272820 Compound DB00683 2655 2664
1019 | 4272820 Compound DB00186 3058 3067
1020 | 4272820 Compound DB00829 3332 3340
1021 | 4272820 Compound DB00829 3462 3470
1022 | 4272820 Compound DB00186 3472 3481
1023 | 4272820 Compound DB00683 3487 3496
1024 | 4272820 Compound DB00186 5897 5906
1025 | 4272820 Compound DB00683 5919 5928
1026 | 4272820 Compound DB00829 5932 5940
1027 | 4272820 Compound DB00829 6415 6423
1028 | 4272820 Compound DB00683 6428 6437
1029 | 4272820 Compound DB00829 6546 6554
1030 | 4272820 Compound DB00683 6585 6594
1031 | 4272820 Compound DB00186 6620 6629
1032 | 4272820 Compound DB00186 6815 6824
1033 | 4272820 Compound DB00683 6903 6912
1034 | 4272820 Compound DB00829 6917 6925
1035 | 4272820 Compound DB00186 7051 7060
1036 | 4272820 Compound DB00186 7087 7096
1037 | 4272820 Compound DB00683 7499 7508
1038 | 4272820 Compound DB00829 7512 7520
1039 | 4272820 Compound DB00186 7539 7548
1040 | 4272820 Compound DB00683 7816 7825
1041 | 4272820 Compound DB00829 7830 7838
1042 | 4272820 Compound DB00186 7932 7941
1043 | 4272820 Compound DB00186 8190 8199
1044 | 4272820 Compound DB00683 8204 8213
1045 | 4272820 Compound DB00683 8349 8358
1046 | 4272820 Compound DB00186 8396 8405
1047 | 4272820 Compound DB00829 8629 8637
1048 | 4272820 Compound DB00683 8726 8735
1049 | 4272820 Compound DB00186 8767 8776
1050 | 4272820 Compound DB00829 8881 8889
1051 | 4272820 Compound DB00186 8894 8903
1052 | 4272820 Compound DB00829 9015 9023
1053 | 4272820 Compound DB00829 9072 9080
1054 | 4272820 Compound DB00186 9139 9148
1055 | 4272820 Compound DB00186 9510 9519
1056 | 4272820 Compound DB00186 10068 10077
1057 | 4272820 Compound DB00186 10351 10360
1058 | 4272820 Compound DB00186 10942 10951
1059 | 4272820 Compound DB00186 10966 10975
1060 | 4272820 Compound DB00186 11152 11161
1061 | 4272820 Compound DB00683 11241 11250
1062 | 4272820 Compound DB00829 11254 11262
1063 | 4272820 Compound DB00683 11470 11479
1064 | 4272820 Compound DB00186 11484 11493
1065 | 4272820 Compound DB00186 12292 12301
1066 | 4272820 Compound DB00683 12490 12499
1067 | 4272820 Compound DB00829 12504 12512
1068 | 4272820 Compound DB00186 12623 12632
1069 | 4272820 Compound DB00186 21395 21404
1070 | 4272820 Compound DB00829 21406 21414
1071 | 4272820 Disease DOID:1826 21465 21483
1072 | 4272820 Disease DOID:1826 21542 21560
1073 | 4272820 Compound DB00683 21562 21571
1074 | 4272820 Compound DB00829 21579 21587
1075 | 4272820 Disease DOID:1826 21609 21627
1076 | 4272820 Compound DB00302 21891 21906
1077 | 4272820 Compound DB00829 22161 22169
1078 | 4272820 Compound DB00186 22174 22183
1079 | 4272820 Compound DB00683 22233 22242
1080 | 4272820 Compound DB00186 22247 22256
1081 | 4272820 Compound DB00186 22534 22543
1082 | 4272820 Compound DB00829 23149 23157
1083 | 4272820 Compound DB00186 23314 23323
1084 | 4272820 Compound DB00683 23487 23496
1085 | 4272821 Gene 55665 1357 1361
1086 | 4272821 Gene 55665 1975 1979
1087 | 4272821 Gene 7857 4230 4234
1088 | 4272821 Gene 392 4737 4741
1089 | 4272821 Gene 55665 5500 5504
1090 | 4272821 Gene 55665 5644 5648
1091 | 4272821 Gene 55665 5716 5720
1092 | 4272821 Gene 55665 5799 5803
1093 | 4272821 Compound DB00994 7101 7109
1094 | 4272821 Compound DB03904 9026 9030
1095 | 4272821 Compound DB03904 9432 9436
1096 | 4272821 Gene 1477 10665 10668
1097 | 4272821 Gene 1854 11060 11068
1098 | 4272821 Compound DB00529 11390 11393
1099 | 4272821 Compound DB09499 11739 11757
1100 | 4272821 Compound DB03166 11919 11930
1101 | 4272821 Compound DB03166 12271 12282
1102 | 4272821 Compound DB00529 12466 12469
1103 | 4272821 Compound DB02772 12509 12516
1104 | 4272821 Gene 8315 13771 13774
1105 | 4272821 Gene 1521 13798 13803
1106 | 4272821 Gene 8315 13919 13922
1107 | 4272821 Compound DB00529 13978 13981
1108 | 4272821 Compound DB03619 13992 14012
1109 | 4272821 Compound DB05780 13992 14012
1110 | 4272821 Compound DB03166 15081 15092
1111 | 4272821 Compound DB03166 15114 15125
1112 | 4272821 Compound DB00151 16000 16008
1113 | 4272821 Compound DB09485 16000 16008
1114 | 4272821 Gene 55665 16839 16843
1115 | 4272821 Gene 997 16896 16899
1116 | 4272821 Gene 997 16952 16955
1117 | 4272821 Gene 1854 19854 19862
1118 | 4272821 Gene 1854 20507 20515
1119 | 4272821 Gene 7857 20519 20523
1120 | 4272821 Gene 1854 21063 21071
1121 | 4272821 Gene 1854 21154 21162
1122 | 4272821 Gene 55665 26686 26690
1123 | 4272821 Gene 55665 27253 27257
1124 | 4272821 Gene 55665 27352 27356
1125 | 4272821 Gene 55665 27543 27547
1126 | 4272821 Compound DB11101 28107 28110
1127 | 4272821 Compound DB11101 28136 28139
1128 | 4272821 Gene 55665 28973 28977
1129 | 4272821 Gene 55665 29021 29025
1130 | 4272821 Gene 55665 29158 29162
1131 | 4272821 Gene 55665 29489 29493
1132 | 4272821 Gene 55665 35569 35573
1133 | 4272821 Gene 55665 35678 35682
1134 | 4272821 Gene 55665 36395 36399
1135 | 4272821 Gene 7857 36931 36935
1136 | 4272821 Gene 55665 40692 40696
1137 | 4272821 Gene 55665 40798 40802
1138 | 4272821 Gene 55665 40978 40982
1139 | 4272821 Gene 55665 41320 41324
1140 | 4272821 Gene 55665 41523 41527
1141 | 4272821 Compound DB00529 43516 43519
1142 | 4272821 Gene 7857 46777 46781
1143 | 4272821 Gene 5144 46791 46796
1144 | 4272821 Gene 55665 47337 47341
1145 | 4272822 Gene 3329 14345 14349
1146 | 4272822 Gene 22999 15000 15005
1147 | 4272822 Gene 9670 16056 16060
1148 | 4272822 Compound DB00065 18261 18265
1149 | 4272822 Compound DB09152 22416 22424
1150 | 4272822 Compound DB00131 23275 23278
1151 | 4272822 Compound DB00640 23275 23278
1152 | 4272822 Compound DB03904 27005 27009
1153 | 4272822 Compound DB00145 28092 28099
1154 | 4272822 Compound DB03904 28136 28140
1155 | 4272822 Compound DB04077 28169 28178
1156 | 4272822 Compound DB09462 28169 28178
1157 | 4272822 Compound DB00898 28377 28384
1158 | 4272822 Compound DB03166 28393 28404
1159 | 4272822 Compound DB00898 28693 28700
1160 | 4272822 Compound DB03843 28939 28951
1161 | 4272822 Compound DB03843 29137 29149
1162 | 4272822 Compound DB00145 29208 29215
1163 | 4272822 Compound DB00134 30967 30977
1164 | 4272822 Disease DOID:9970 35033 35040
1165 | 4272822 Gene 3329 35193 35197
1166 | 4272822 Gene 22999 35441 35456
1167 | 4272822 Gene 22999 35563 35578
1168 | 4272822 Disease DOID:2994 35856 35865
1169 | 4272822 Gene 136 35978 35988
1170 | 4272822 Compound DB00065 36954 36958
1171 | 4272822 Disease DOID:1324 37265 37291
1172 | 4272823 Disease DOID:10283 60 75
1173 | 4272823 Disease DOID:10283 125 140
1174 | 4272823 Disease DOID:10283 474 489
1175 | 4272823 Disease DOID:10283 560 585
1176 | 4272823 Disease DOID:10283 2526 2541
1177 | 4272823 Disease DOID:10283 4997 5012
1178 | 4272823 Disease DOID:10283 5033 5048
1179 | 4272823 Disease DOID:10283 5096 5111
1180 | 4272823 Disease DOID:10283 5847 5872
1181 | 4272823 Disease DOID:10283 6562 6587
1182 | 4272823 Disease DOID:10283 6682 6697
1183 | 4272823 Gene 1068 7509 7512
1184 | 4272823 Disease DOID:10283 12066 12081
1185 | 4272823 Compound DB00936 12342 12349
1186 | 4272823 Compound DB00945 12342 12349
1187 | 4272823 Disease DOID:10283 14250 14265
1188 | 4272823 Disease DOID:10283 15815 15830
1189 | 4272823 Disease DOID:10283 16390 16405
1190 | 4272823 Disease DOID:10283 18807 18822
1191 | 4272823 Disease DOID:10283 19733 19748
1192 | 4272823 Disease DOID:10283 21825 21840
1193 | 4272823 Disease DOID:10283 24648 24663
1194 | 4272823 Disease DOID:10652 29484 29486
1195 | 4272823 Disease DOID:10283 29975 29990
1196 | 4272823 Disease DOID:10283 30043 30058
1197 | 4272823 Disease DOID:10283 30179 30204
1198 | 4272823 Disease DOID:10283 30327 30342
1199 | 4272823 Disease DOID:10283 30385 30400
1200 | 4272823 Disease DOID:10283 30467 30482
1201 | 4272823 Disease DOID:10283 30574 30589
1202 | 4272823 Disease DOID:10283 30862 30877
1203 | 4272823 Disease DOID:10283 31035 31050
1204 | 4272823 Disease DOID:10283 31240 31255
1205 | 4272823 Disease DOID:10283 31318 31333
1206 | 4272823 Disease DOID:10283 31465 31490
1207 | 4272823 Disease DOID:10283 31538 31553
1208 | 4272823 Disease DOID:10283 32431 32456
1209 | 4272823 Disease DOID:10283 32643 32658
1210 | 4272823 Disease DOID:10283 32685 32700
1211 | 4272823 Disease DOID:10283 32843 32858
1212 | 4272823 Disease DOID:10283 32917 32942
1213 | 4272823 Disease DOID:10283 33016 33041
1214 | 4272823 Disease DOID:10283 33163 33188
1215 | 4272823 Disease DOID:10283 33293 33318
1216 | 4272823 Disease DOID:10283 33468 33483
1217 | 4272823 Disease DOID:10283 33544 33567
1218 | 4272823 Disease DOID:10283 33730 33745
1219 | 4272823 Disease DOID:10283 34088 34113
1220 | 4272823 Disease DOID:10283 34201 34226
1221 | 4272823 Disease DOID:10283 34372 34387
1222 | 4272823 Disease DOID:10283 34486 34501
1223 | 4272823 Disease DOID:10283 34569 34584
1224 | 4272823 Disease DOID:10283 34784 34809
1225 | 4272823 Disease DOID:10283 34901 34916
1226 | 4272823 Disease DOID:10283 34967 34982
1227 | 4272823 Disease DOID:10283 35040 35067
1228 | 4272823 Disease DOID:10283 35353 35378
1229 | 4272824 Compound DB00907 39 46
1230 | 4272824 Compound DB00907 227 234
1231 | 4272824 Compound DB01579 279 294
1232 | 4272824 Compound DB01576 299 312
1233 | 4272824 Compound DB00907 335 342
1234 | 4272824 Compound DB00907 364 371
1235 | 4272824 Compound DB00907 518 525
1236 | 4272824 Compound DB00907 767 774
1237 | 4272824 Compound DB00907 1021 1028
1238 | 4272824 Compound DB00907 1095 1102
1239 | 4272824 Compound DB00907 1617 1624
1240 | 4272824 Compound DB00907 1693 1700
1241 | 4272824 Compound DB00907 1849 1856
1242 | 4272824 Compound DB00907 2760 2767
1243 | 4272824 Compound DB00907 3716 3723
1244 | 4272824 Compound DB00907 3884 3891
1245 | 4272824 Compound DB00907 4000 4007
1246 | 4272824 Compound DB00907 4214 4221
1247 | 4272824 Compound DB00907 4326 4333
1248 | 4272824 Compound DB00907 4820 4827
1249 | 4272824 Compound DB00907 5326 5333
1250 | 4272824 Compound DB00907 5569 5576
1251 | 4272824 Compound DB00907 5693 5700
1252 | 4272824 Compound DB01576 5747 5760
1253 | 4272824 Compound DB01579 5762 5777
1254 | 4272824 Compound DB00830 5783 5796
1255 | 4272824 Compound DB00907 7688 7695
1256 | 4272824 Compound DB00907 7985 7992
1257 | 4272824 Compound DB00907 8367 8374
1258 | 4272824 Compound DB00907 8470 8477
1259 | 4272824 Compound DB00907 8545 8552
1260 | 4272824 Compound DB01576 9161 9174
1261 | 4272824 Compound DB01579 9196 9215
1262 | 4272824 Compound DB00830 9238 9255
1263 | 4272824 Compound DB09153 9324 9330
1264 | 4272824 Compound DB00907 9401 9408
1265 | 4272824 Compound DB00907 9533 9540
1266 | 4272824 Compound DB00907 9785 9792
1267 | 4272824 Compound DB00907 9836 9843
1268 | 4272824 Compound DB00907 10065 10072
1269 | 4272824 Compound DB00907 10189 10196
1270 | 4272824 Compound DB00907 10265 10272
1271 | 4272824 Compound DB00907 10907 10914
1272 | 4272824 Compound DB00907 11232 11239
1273 | 4272824 Compound DB00907 13405 13412
1274 | 4272824 Compound DB01576 14224 14237
1275 | 4272824 Compound DB00907 14271 14278
1276 | 4272824 Compound DB01576 14380 14393
1277 | 4272824 Compound DB00907 14439 14446
1278 | 4272824 Compound DB01576 14488 14501
1279 | 4272824 Compound DB01576 14565 14578
1280 | 4272824 Compound DB01576 14754 14767
1281 | 4272824 Compound DB01579 14990 15009
1282 | 4272824 Compound DB00907 15043 15050
1283 | 4272824 Compound DB01579 15152 15167
1284 | 4272824 Compound DB00907 15228 15235
1285 | 4272824 Compound DB01579 15277 15296
1286 | 4272824 Compound DB01579 15419 15438
1287 | 4272824 Compound DB01579 15555 15574
1288 | 4272824 Compound DB00830 15932 15949
1289 | 4272824 Compound DB00907 15983 15990
1290 | 4272824 Compound DB00830 16092 16105
1291 | 4272824 Compound DB00907 16165 16172
1292 | 4272824 Compound DB00830 16214 16231
1293 | 4272824 Compound DB00830 16482 16499
1294 | 4272824 Compound DB00907 16578 16585
1295 | 4272824 Compound DB00907 16643 16650
1296 | 4272824 Compound DB00907 16759 16766
1297 | 4272824 Compound DB00907 16858 16865
1298 | 4272824 Compound DB00907 17060 17067
1299 | 4272824 Disease DOID:1826 17657 17661
1300 | 4272824 Disease DOID:1826 17729 17733
1301 | 4272824 Compound DB00907 17994 18001
1302 | 4272824 Compound DB00907 19759 19766
1303 | 4272824 Compound DB09153 21246 21252
1304 | 4272824 Compound DB00907 21276 21283
1305 | 4272824 Compound DB00907 21321 21328
1306 | 4272824 Compound DB00907 21373 21380
1307 | 4272824 Compound DB00907 21550 21557
1308 | 4272824 Compound DB00907 21826 21833
1309 | 4272824 Compound DB00907 22361 22368
1310 | 4272824 Compound DB00907 22452 22459
1311 | 4272824 Compound DB00907 22517 22524
1312 | 4272824 Compound DB00907 22584 22591
1313 | 4272824 Compound DB01576 22931 22944
1314 | 4272824 Compound DB00907 23075 23082
1315 | 4272824 Compound DB00907 23169 23176
1316 | 4272824 Compound DB00907 23199 23206
1317 | 4272824 Compound DB00907 23322 23329
1318 | 4272824 Compound DB00907 23358 23365
1319 | 4272824 Compound DB00907 23413 23420
1320 | 4272824 Compound DB01576 23470 23483
1321 | 4272824 Compound DB00907 23729 23736
1322 | 4272824 Compound DB00907 24013 24020
1323 | 4272824 Compound DB09153 24136 24142
1324 | 4272824 Compound DB00907 24372 24379
1325 | 4272824 Compound DB00907 24593 24600
1326 | 4272824 Compound DB00907 25462 25469
1327 | 4272824 Compound DB01576 25697 25710
1328 | 4272824 Compound DB00907 25980 25987
1329 | 4272824 Compound DB00907 26325 26332
1330 | 4272824 Compound DB01576 26791 26804
1331 | 4272824 Compound DB01579 26809 26824
1332 | 4272824 Compound DB00907 26898 26905
1333 | 4272824 Compound DB01576 27051 27064
1334 | 4272824 Compound DB01579 27069 27084
1335 | 4272824 Compound DB00907 28035 28042
1336 | 4272824 Compound DB00182 28376 28387
1337 | 4272824 Compound DB00907 28401 28408
1338 | 4272824 Compound DB00988 28541 28549
1339 | 4272824 Compound DB00368 28550 28564
1340 | 4272824 Compound DB00907 28600 28607
1341 | 4272824 Compound DB00907 28814 28821
1342 | 4272824 Compound DB01579 28907 28922
1343 | 4272824 Compound DB00907 28941 28948
1344 | 4272824 Compound DB00907 29695 29702
1345 | 4272824 Compound DB00898 29815 29822
1346 | 4272824 Compound DB00898 29847 29854
1347 | 4272824 Compound DB00907 30402 30409
1348 | 4272824 Compound DB00907 30801 30808
1349 | 4272824 Compound DB00907 31019 31026
1350 | 4272824 Compound DB01576 31073 31086
1351 | 4272824 Compound DB00907 31100 31107
1352 | 4272824 Compound DB00184 31389 31397
1353 | 4272824 Compound DB00907 31702 31709
1354 | 4272824 Compound DB00907 31813 31820
1355 | 4272824 Compound DB00907 32303 32310
1356 | 4272824 Compound DB00907 32336 32343
1357 | 4272824 Compound DB01576 32386 32399
1358 | 4272824 Compound DB00907 32433 32440
1359 | 4272824 Compound DB01576 32542 32555
1360 | 4272824 Compound DB00907 32671 32678
1361 | 4272824 Compound DB01576 32801 32814
1362 | 4272824 Compound DB01579 33065 33084
1363 | 4272824 Compound DB00907 33118 33125
1364 | 4272824 Compound DB01579 33227 33246
1365 | 4272824 Compound DB00907 33362 33369
1366 | 4272824 Compound DB01579 33492 33511
1367 | 4272824 Compound DB00830 33762 33779
1368 | 4272824 Compound DB00907 33813 33820
1369 | 4272824 Compound DB00830 33922 33939
1370 | 4272824 Compound DB00907 34055 34062
1371 | 4272824 Compound DB00830 34185 34202
1372 | 4272824 Compound DB00907 34451 34458
1373 | 4272824 Compound DB00907 34482 34489
1374 | 4272824 Compound DB00907 34715 34722
1375 | 4272824 Compound DB00830 34845 34862
1376 | 4272824 Compound DB01576 35105 35118
1377 | 4272824 Compound DB00907 35151 35158
1378 | 4272824 Compound DB00907 35388 35395
1379 | 4272824 Compound DB00907 35436 35443
1380 | 4272824 Compound DB00830 39820 39837
1381 | 4272825 Compound DB08820 12 21
1382 | 4272825 Compound DB09280 231 241
1383 | 4272825 Compound DB09280 243 249
1384 | 4272825 Compound DB08820 323 332
1385 | 4272825 Disease DOID:1793 2276 2284
1386 | 4272825 Compound DB08820 3269 3275
1387 | 4272825 Compound DB08820 3277 3286
1388 | 4272825 Compound DB09280 4889 4895
1389 | 4272825 Compound DB09280 4897 4907
1390 | 4272825 Compound DB09280 5035 5041
1391 | 4272825 Compound DB08820 6870 6876
1392 | 4272825 Disease DOID:3083 6953 6990
1393 | 4272825 Disease DOID:3083 6992 6996
1394 | 4272825 Compound DB00594 7969 7978
1395 | 4272825 Compound DB00594 8654 8663
1396 | 4272825 Compound DB09280 9558 9564
1397 | 4272825 Compound DB09280 10176 10182
1398 | 4272825 Compound DB09280 10316 10322
1399 | 4272825 Compound DB09280 11590 11596
1400 | 4272825 Compound DB09280 12393 12399
1401 | 4272825 Compound DB08820 15926 15932
1402 | 4272825 Compound DB00594 15977 15986
1403 | 4272825 Compound DB01093 16542 16546
1404 | 4272825 Gene 788 16690 16693
1405 | 4272825 Compound DB00594 16745 16754
1406 | 4272825 Compound DB00646 16964 16972
1407 | 4272825 Gene 788 17220 17223
1408 | 4272825 Gene 6267 17531 17534
1409 | 4272825 Gene 6268 18080 18083
1410 | 4272825 Compound DB00171 19118 19121
1411 | 4272825 Compound DB00640 19118 19121
1412 | 4272825 Compound DB09280 21313 21319
1413 | 4272825 Compound DB09280 21527 21533
1414 | 4272825 Disease DOID:3083 24758 24795
1415 | 4272825 Disease DOID:3083 24797 24801
1416 | 4272825 Disease DOID:3083 24968 24972
1417 | 4272825 Compound DB08820 25156 25162
1418 | 4272825 Disease DOID:3083 25722 25726
1419 | 4272825 Compound DB00594 27495 27504
1420 | 4272825 Compound DB09280 29680 29686
1421 | 4272825 Compound DB08820 29723 29729
1422 | 4272825 Gene 3071 32871 32874
1423 | 4272825 Compound DB09280 33351 33357
1424 | 4272825 Compound DB03843 33723 33731
1425 | 4272825 Compound DB00065 34154 34158
1426 | 4272825 Compound DB09341 34210 34217
1427 | 4272825 Compound DB11280 34210 34217
1428 | 4272825 Compound DB00594 34571 34580
1429 | 4272825 Compound DB08820 34654 34660
1430 | 4272825 Compound DB00646 34854 34862
1431 | 4272825 Compound DB00594 37066 37075
1432 | 4272825 Compound DB00594 37240 37249
1433 | 4272825 Compound DB00594 37543 37552
1434 | 4272825 Gene 788 38185 38188
1435 | 4272825 Compound DB00646 38221 38229
1436 | 4272825 Gene 6267 38312 38315
1437 | 4272825 Gene 6268 38391 38394
1438 | 4272825 Compound DB00203 40393 40403
1439 | 4272825 Compound DB08820 41099 41108
1440 | 4272825 Compound DB08820 41305 41314
1441 | 4272825 Compound DB08820 41576 41585
1442 | 4272825 Compound DB00646 43138 43146
1443 | 4272825 Compound DB08820 45285 45294
1444 | 4272825 Compound DB08820 45338 45347
1445 | 4272825 Compound DB08820 45529 45538
1446 | 4272825 Compound DB08820 45984 45993
1447 | 4272825 Compound DB00065 46104 46108
1448 | 4272825 Compound DB00065 46275 46279
1449 | 4272825 Compound DB08820 46464 46473
1450 | 4272825 Compound DB01093 47487 47491
1451 | 4272825 Compound DB01093 48197 48201
1452 | 4272825 Compound DB01093 52058 52062
1453 | 4272825 Compound DB08820 52140 52146
1454 | 4272825 Compound DB00646 53018 53026
1455 | 4272825 Compound DB00646 53155 53163
1456 | 4272825 Compound DB08820 53647 53653
1457 | 4272826 Disease DOID:2531 104 113
1458 | 4272826 Disease DOID:2531 181 190
1459 | 4272826 Gene 11214 603 607
1460 | 4272826 Disease DOID:2531 775 784
1461 | 4272826 Disease DOID:2531 1098 1107
1462 | 4272826 Disease DOID:2531 1149 1158
1463 | 4272826 Disease DOID:2531 1418 1427
1464 | 4272826 Disease DOID:2531 1581 1589
1465 | 4272826 Disease DOID:2531 1761 1769
1466 | 4272826 Disease DOID:2531 1898 1906
1467 | 4272826 Gene 11214 2009 2013
1468 | 4272826 Disease DOID:2531 2086 2094
1469 | 4272826 Disease DOID:2531 2212 2221
1470 | 4272826 Disease DOID:2531 2293 2302
1471 | 4272826 Disease DOID:2531 2532 2541
1472 | 4272826 Disease DOID:2531 2654 2663
1473 | 4272826 Disease DOID:2531 2722 2731
1474 | 4272826 Disease DOID:2531 2864 2873
1475 | 4272826 Disease DOID:2531 2993 3002
1476 | 4272826 Disease DOID:2531 3169 3177
1477 | 4272826 Compound DB00759 3531 3543
1478 | 4272826 Compound DB00759 3593 3605
1479 | 4272826 Disease DOID:2531 4478 4496
1480 | 4272826 Disease DOID:2531 5058 5066
1481 | 4272826 Disease DOID:2531 6664 6672
1482 | 4272826 Disease DOID:2531 6825 6834
1483 | 4272826 Disease DOID:2531 7057 7066
1484 | 4272826 Disease DOID:2531 7071 7080
1485 | 4272826 Disease DOID:2531 7090 7108
1486 | 4272826 Disease DOID:2531 7206 7215
1487 | 4272826 Disease DOID:2531 7256 7265
1488 | 4272826 Disease DOID:2531 7315 7323
1489 | 4272826 Disease DOID:2531 7393 7402
1490 | 4272826 Disease DOID:2531 7454 7463
1491 | 4272826 Disease DOID:2531 7567 7576
1492 | 4272826 Disease DOID:2531 7662 7671
1493 | 4272826 Gene 11214 7860 7864
1494 | 4272826 Disease DOID:2531 7888 7897
1495 | 4272826 Gene 11214 7998 8002
1496 | 4272826 Gene 11214 8187 8191
1497 | 4272826 Disease DOID:2531 8207 8216
1498 | 4272826 Disease DOID:2531 8341 8350
1499 | 4272826 Disease DOID:2531 8396 8405
1500 | 4272826 Disease DOID:2531 8654 8663
1501 | 4272826 Disease DOID:2531 8859 8868
1502 | 4272826 Disease DOID:2531 8954 8963
1503 | 4272826 Disease DOID:2531 9685 9694
1504 | 4272826 Disease DOID:2531 10149 10158
1505 | 4272826 Disease DOID:2531 10461 10470
1506 | 4272826 Disease DOID:2531 10674 10682
1507 | 4272826 Disease DOID:2531 10735 10744
1508 | 4272826 Disease DOID:2531 10873 10882
1509 | 4272826 Disease DOID:2531 10983 10992
1510 | 4272826 Disease DOID:2531 11018 11027
1511 | 4272826 Disease DOID:2531 11166 11175
1512 | 4272826 Disease DOID:2531 11376 11385
1513 | 4272826 Disease DOID:2531 11491 11500
1514 | 4272826 Disease DOID:2531 11949 11958
1515 | 4272826 Disease DOID:2531 12222 12231
1516 | 4272826 Disease DOID:2531 12376 12385
1517 | 4272826 Disease DOID:2531 12618 12627
1518 | 4272826 Disease DOID:2531 12771 12780
1519 | 4272826 Disease DOID:2531 12878 12887
1520 | 4272826 Disease DOID:2531 13266 13275
1521 | 4272826 Disease DOID:2531 13511 13520
1522 | 4272826 Disease DOID:2531 13623 13632
1523 | 4272826 Disease DOID:2531 13667 13676
1524 | 4272826 Disease DOID:2531 13911 13920
1525 | 4272826 Disease DOID:2531 14299 14308
1526 | 4272826 Disease DOID:2531 14483 14492
1527 | 4272826 Disease DOID:2531 14669 14677
1528 | 4272826 Disease DOID:2531 14735 14744
1529 | 4272826 Disease DOID:2531 14850 14859
1530 | 4272826 Disease DOID:2531 15029 15038
1531 | 4272826 Disease DOID:2531 15064 15073
1532 | 4272826 Disease DOID:2531 15287 15296
1533 | 4272826 Disease DOID:2531 15424 15433
1534 | 4272826 Disease DOID:2531 15622 15631
1535 | 4272826 Gene 11214 16527 16531
1536 | 4272826 Gene 11214 16577 16581
1537 | 4272826 Disease DOID:2531 16627 16636
1538 | 4272826 Disease DOID:2531 16823 16832
1539 | 4272826 Disease DOID:2531 17665 17674
1540 | 4272826 Disease DOID:2531 17797 17806
1541 | 4272826 Disease DOID:2531 17887 17896
1542 | 4272826 Disease DOID:2531 17996 18005
1543 | 4272826 Gene 3854 18231 18235
1544 | 4272826 Disease DOID:2531 18891 18900
1545 | 4272826 Disease DOID:2531 19108 19117
1546 | 4272826 Disease DOID:2531 19322 19331
1547 | 4272826 Gene 3854 19775 19802
1548 | 4272826 Gene 3854 19804 19808
1549 | 4272826 Disease DOID:2531 20067 20076
1550 | 4272826 Gene 3854 20176 20180
1551 | 4272826 Disease DOID:2531 20428 20454
1552 | 4272826 Disease DOID:2531 22094 22135
1553 | 4272826 Gene 4072 22240 22244
1554 | 4272826 Disease DOID:0060073 22264 22285
1555 | 4272826 Disease DOID:2531 22354 22377
1556 | 4272826 Disease DOID:2531 22407 22429
1557 | 4272826 Gene 9762 22431 22435
1558 | 4272826 Gene 3783 22474 22481
1559 | 4272826 Disease DOID:2531 22519 22539
1560 | 4272826 Disease DOID:2531 22719 22728
1561 | 4272826 Disease DOID:2531 22884 22906
1562 | 4272826 Disease DOID:2531 22942 22964
1563 | 4272826 Gene 4051 23011 23048
1564 | 4272826 Gene 4051 23050 23053
1565 | 4272826 Gene 3014 23142 23146
1566 | 4272826 Gene 1549 23191 23196
1567 | 4272826 Disease DOID:2531 24573 24582
1568 | 4272826 Disease DOID:2531 25644 25652
1569 | 4272826 Gene 11214 25760 25764
1570 | 4272826 Disease DOID:2531 25832 25841
1571 | 4272826 Disease DOID:2531 26129 26145
1572 | 4272826 Disease DOID:2531 26244 26253
1573 | 4272826 Disease DOID:2531 26308 26326
1574 | 4272826 Disease DOID:2531 26531 26549
1575 | 4272826 Gene 1945 26857 26863
1576 | 4272826 Gene 3854 27572 27576
1577 | 4272826 Gene 3854 27580 27584
1578 | 4272826 Gene 3854 27586 27590
1579 | 4272826 Disease DOID:4989 28082 28092
1580 | 4272826 Disease DOID:2531 28219 28228
1581 | 4272826 Gene 3854 28372 28377
1582 | 4272826 Disease DOID:2531 28438 28446
1583 | 4272826 Gene 10990 28643 28648
1584 | 4272826 Gene 4072 29065 29069
1585 | 4272826 Disease DOID:2531 29124 29132
1586 | 4272826 Disease DOID:2531 29172 29200
1587 | 4272826 Gene 4072 29236 29240
1588 | 4272826 Disease DOID:2531 29346 29362
1589 | 4272826 Gene 3783 29408 29415
1590 | 4272826 Gene 9762 29441 29445
1591 | 4272826 Disease DOID:2531 29512 29520
1592 | 4272826 Disease DOID:2531 29799 29821
1593 | 4272826 Disease DOID:2531 29875 29878
1594 | 4272826 Gene 4051 29890 29893
1595 | 4272826 Disease DOID:2531 30039 30055
1596 | 4272826 Gene 2891 30129 30133
1597 | 4272826 Disease DOID:2531 30288 30296
1598 | 4272826 Disease DOID:2531 30373 30382
1599 | 4272826 Disease DOID:2531 30494 30503
1600 | 4272826 Disease DOID:2531 30574 30583
1601 | 4272826 Disease DOID:2531 30767 30776
1602 | 4272826 Disease DOID:2531 31165 31174
1603 | 4272826 Disease DOID:2531 31471 31480
1604 | 4272826 Disease DOID:2531 31611 31620
1605 | 4272826 Disease DOID:2531 31698 31707
1606 | 4272826 Disease DOID:2531 31859 31868
1607 | 4272826 Disease DOID:2531 31980 31989
1608 | 4272826 Disease DOID:2531 32059 32068
1609 | 4272826 Disease DOID:2531 32281 32290
1610 | 4272826 Disease DOID:2531 32678 32687
1611 | 4272826 Disease DOID:2531 32976 32985
1612 | 4272826 Gene 586 33176 33179
1613 | 4272826 Gene 586 33254 33257
1614 | 4272826 Disease DOID:2531 33360 33369
1615 | 4272826 Disease DOID:2531 33711 33720
1616 | 4272826 Disease DOID:2531 33832 33841
1617 | 4272826 Disease DOID:2531 33908 33917
1618 | 4272826 Disease DOID:2531 34230 34238
1619 | 4272826 Disease DOID:2531 34517 34525
1620 | 4272826 Disease DOID:2531 34646 34655
1621 | 4272826 Disease DOID:2531 34718 34726
1622 | 4272826 Disease DOID:2531 35009 35018
1623 | 4272826 Disease DOID:2531 35434 35443
1624 | 4272826 Disease DOID:2531 36157 36166
1625 | 4272826 Disease DOID:2531 36210 36219
1626 | 4272826 Disease DOID:2531 36346 36381
1627 | 4272826 Disease DOID:2531 37751 37759
1628 | 4272826 Disease DOID:2531 38023 38031
1629 | 4272826 Disease DOID:2531 38107 38115
1630 | 4272826 Disease DOID:2531 38528 38600
1631 | 4272826 Gene 4072 39126 39130
1632 | 4272826 Gene 9762 39357 39361
1633 | 4272826 Gene 3014 40021 40025
1634 | 4272826 Gene 1549 40140 40145
1635 | 4272827 Disease DOID:6364 3254 3277
1636 | 4272827 Disease DOID:10763 8424 8436
1637 | 4272827 Disease DOID:2841 8451 8457
1638 | 4272827 Gene 55534 10416 10419
1639 | 4272827 Disease DOID:9970 12653 12660
1640 | 4272827 Disease DOID:10763 13699 13711
1641 | 4272827 Disease DOID:2841 13713 13719
1642 | 4272827 Gene 55534 14878 14881
1643 | 4272827 Disease DOID:9970 25028 25035
1644 | 4272828 Disease DOID:3393 3881 3902
1645 | 4272828 Disease DOID:2531 4069 4084
1646 | 4272828 Disease DOID:2355 4110 4145
1647 | 4272828 Disease DOID:3083 9516 9553
1648 | 4272828 Disease DOID:3393 10312 10333
1649 | 4272828 Compound DB01225 12312 12322
1650 | 4272828 Compound DB01225 12451 12461
1651 | 4272829 Disease DOID:11476 1376 1388
1652 | 4272829 Disease DOID:11476 1470 1482
1653 | 4272829 Disease DOID:9970 1869 1876
1654 | 4272829 Disease DOID:9970 2454 2459
1655 | 4272829 Disease DOID:9970 4195 4200
1656 | 4272829 Disease DOID:11476 4499 4511
1657 | 4272829 Disease DOID:11476 4571 4583
1658 | 4272829 Disease DOID:9970 5895 5900
1659 | 4272829 Disease DOID:9970 5950 5955
1660 | 4272829 Disease DOID:11476 7723 7735
1661 | 4272829 Gene 173 7993 8000
1662 | 4272829 Disease DOID:9970 8166 8173
1663 | 4272829 Disease DOID:9970 8705 8710
1664 | 4272829 Disease DOID:9970 8957 8962
1665 | 4272829 Disease DOID:11476 9705 9717
1666 | 4272829 Disease DOID:11476 9814 9826
1667 | 4272829 Disease DOID:11476 10671 10695
1668 | 4272829 Disease DOID:9970 11069 11074
1669 | 4272829 Disease DOID:9970 11236 11243
1670 | 4272829 Disease DOID:11476 11259 11271
1671 | 4272829 Disease DOID:9970 11386 11393
1672 | 4272829 Disease DOID:9970 11701 11708
1673 | 4272829 Disease DOID:9970 11819 11826
1674 | 4272830 Disease DOID:1826 4209 4219
1675 | 4272830 Disease DOID:1826 4258 4269
1676 | 4272830 Disease DOID:1826 5706 5714
1677 | 4272830 Compound DB01212 5902 5913
1678 | 4272830 Compound DB00479 6099 6107
1679 | 4272830 Compound DB00798 6111 6121
1680 | 4272830 Compound DB00479 6123 6131
1681 | 4272830 Compound DB01015 6192 6208
1682 | 4272830 Compound DB00440 6213 6225
1683 | 4272830 Compound DB01212 6442 6453
1684 | 4272830 Compound DB00479 6474 6482
1685 | 4272830 Compound DB00798 6486 6496
1686 | 4272831 Disease DOID:585 2640 2655
1687 | 4272831 Compound DB00624 3655 3667
1688 | 4272831 Compound DB04272 3735 3742
1689 | 4272831 Disease DOID:11819 5629 5642
1690 | 4272831 Compound DB00138 9715 9722
1691 | 4272831 Compound DB00138 25251 25258
1692 | 4272832 Compound DB00281 7765 7774
1693 | 4272832 Compound DB00281 8671 8680
1694 | 4272832 Compound DB06812 9232 9247
1695 | 4272832 Compound DB01109 14906 14913
1696 | 4272832 Compound DB01109 18708 18715
1697 | 4272833 Disease DOID:263 67 89
1698 | 4272833 Disease DOID:263 198 211
1699 | 4272833 Disease DOID:263 1543 1556
1700 | 4272833 Disease DOID:263 1691 1704
1701 | 4272833 Disease DOID:784 1709 1732
1702 | 4272833 Disease DOID:263 1928 1941
1703 | 4272833 Disease DOID:263 2703 2720
1704 | 4272833 Disease DOID:263 9169 9182
1705 | 4272833 Disease DOID:263 9504 9515
1706 | 4272833 Disease DOID:263 9517 9528
1707 | 4272833 Disease DOID:263 9621 9632
1708 | 4272833 Disease DOID:263 9671 9683
1709 | 4272833 Disease DOID:263 15603 15616
1710 | 4272833 Disease DOID:263 15804 15817
1711 | 4272833 Compound DB00898 17362 17369
1712 | 4272833 Compound DB00898 17638 17645
1713 | 4272833 Compound DB00898 17742 17749
1714 | 4272834 Disease DOID:2531 54 69
1715 | 4272834 Disease DOID:2531 427 430
1716 | 4272834 Disease DOID:2531 670 695
1717 | 4272834 Disease DOID:2531 1013 1036
1718 | 4272834 Disease DOID:2531 1690 1698
1719 | 4272834 Disease DOID:2531 1987 2012
1720 | 4272834 Disease DOID:2531 2261 2283
1721 | 4272834 Disease DOID:2531 2285 2288
1722 | 4272834 Disease DOID:2531 3269 3272
1723 | 4272834 Disease DOID:2531 3367 3370
1724 | 4272834 Compound DB00158 4204 4210
1725 | 4272834 Disease DOID:2531 4306 4309
1726 | 4272834 Disease DOID:2531 4354 4357
1727 | 4272834 Disease DOID:2531 4420 4423
1728 | 4272834 Disease DOID:2531 4793 4796
1729 | 4272834 Disease DOID:2531 5135 5138
1730 | 4272834 Disease DOID:2531 5190 5193
1731 | 4272834 Disease DOID:2355 5254 5260
1732 | 4272834 Disease DOID:2531 5365 5368
1733 | 4272834 Disease DOID:2531 5458 5466
1734 | 4272834 Disease DOID:2355 5566 5572
1735 | 4272834 Disease DOID:2531 5605 5608
1736 | 4272834 Disease DOID:2531 5651 5654
1737 | 4272834 Disease DOID:2531 6320 6323
1738 | 4272834 Disease DOID:2531 6482 6485
1739 | 4272834 Disease DOID:2531 6533 6536
1740 | 4272834 Disease DOID:2531 6622 6625
1741 | 4272834 Disease DOID:2531 6647 6650
1742 | 4272834 Disease DOID:2531 7330 7333
1743 | 4272834 Disease DOID:2531 7513 7516
1744 | 4272834 Disease DOID:2531 7595 7598
1745 | 4272834 Disease DOID:10763 7666 7678
1746 | 4272834 Disease DOID:2531 7786 7798
1747 | 4272834 Disease DOID:2531 7865 7868
1748 | 4272834 Disease DOID:3083 7899 7931
1749 | 4272834 Disease DOID:2531 8036 8039
1750 | 4272834 Disease DOID:2531 8058 8061
1751 | 4272834 Disease DOID:2531 8112 8115
1752 | 4272834 Disease DOID:2531 8366 8391
1753 | 4272834 Disease DOID:2531 8894 8917
1754 | 4272834 Compound DB01592 9177 9181
1755 | 4272834 Compound DB01592 9825 9829
1756 | 4272834 Disease DOID:2531 10064 10072
1757 | 4272834 Disease DOID:2531 10233 10236
1758 | 4272834 Disease DOID:2355 10681 10687
1759 | 4272834 Disease DOID:2531 10852 10875
1760 | 4272834 Disease DOID:2355 11317 11329
1761 | 4272834 Disease DOID:2355 11931 11937
1762 | 4272834 Disease DOID:2355 11946 11952
1763 | 4272834 Disease DOID:2355 11976 11982
1764 | 4272834 Disease DOID:2355 12099 12108
1765 | 4272834 Disease DOID:2355 12132 12141
1766 | 4272834 Disease DOID:2531 12563 12566
1767 | 4272834 Disease DOID:2531 16267 16270
1768 | 4272834 Disease DOID:2531 17048 17073
1769 | 4272834 Disease DOID:2531 17078 17093
1770 | 4272834 Disease DOID:2531 17095 17123
1771 | 4272834 Disease DOID:2531 17124 17139
1772 | 4272834 Disease DOID:2531 17236 17251
1773 | 4272834 Disease DOID:2531 17302 17327
1774 | 4272834 Disease DOID:2531 17385 17410
1775 | 4272834 Compound DB01592 17464 17468
1776 | 4272834 Disease DOID:2531 17517 17520
1777 | 4272834 Disease DOID:2355 17545 17551
1778 | 4272834 Disease DOID:2531 17556 17607
1779 | 4272834 Disease DOID:2531 17620 17633
1780 | 4272834 Disease DOID:2531 17634 17658
1781 | 4272834 Disease DOID:2531 17734 17759
1782 | 4272834 Disease DOID:2531 17802 17827
1783 | 4272834 Disease DOID:2355 17852 17858
1784 | 4272834 Disease DOID:2531 17891 17916
1785 | 4272834 Disease DOID:2531 18004 18029
1786 | 4272834 Disease DOID:2531 18155 18170
1787 | 4272834 Compound DB01592 18229 18233
1788 | 4272834 Disease DOID:2531 18247 18272
1789 | 4272834 Disease DOID:2531 18339 18364
1790 | 4272834 Disease DOID:2531 18491 18494
1791 | 4272834 Disease DOID:2355 18499 18514
1792 | 4272834 Compound DB01592 18549 18553
1793 | 4272834 Compound DB01592 18586 18590
1794 | 4272834 Disease DOID:2531 18639 18663
1795 | 4272834 Disease DOID:2531 18778 18803
1796 | 4272834 Disease DOID:2531 18882 18907
1797 | 4272834 Disease DOID:2531 18956 18981
1798 | 4272834 Gene 9098 19004 19009
1799 | 4272834 Gene 3802 19011 19014
1800 | 4272834 Gene 3040 19016 19020
1801 | 4272834 Gene 81697 19045 19049
1802 | 4272834 Gene 55661 19051 19055
1803 | 4272834 Disease DOID:2531 19086 19111
1804 | 4272834 Disease DOID:2531 19116 19139
1805 | 4272834 Disease DOID:2531 19167 19182
1806 | 4272834 Disease DOID:2531 19303 19327
1807 | 4272834 Disease DOID:2531 19438 19474
1808 | 4272834 Disease DOID:2531 19508 19523
1809 | 4272834 Disease DOID:2531 19664 19688
1810 | 4272834 Disease DOID:2531 19745 19771
1811 | 4272834 Disease DOID:2531 19796 19821
1812 | 4272834 Disease DOID:2531 19866 19891
1813 | 4272834 Disease DOID:2531 19908 19933
1814 | 4272834 Disease DOID:2531 19946 19974
1815 | 4272834 Disease DOID:2531 20215 20248
1816 | 4272834 Disease DOID:2531 20250 20253
1817 | 4272834 Disease DOID:2531 20330 20355
1818 | 4272834 Disease DOID:2531 20364 20379
1819 | 4272834 Disease DOID:2531 20456 20480
1820 | 4272834 Disease DOID:2531 20485 20500
1821 | 4272834 Disease DOID:2531 20597 20622
1822 | 4272834 Compound DB00928 20636 20647
1823 | 4272834 Disease DOID:2531 20690 20705
1824 | 4272834 Disease DOID:2531 20813 20838
1825 | 4272836 Disease DOID:824 4167 4180
1826 | 4272836 Disease DOID:216 4363 4376
1827 | 4272836 Gene 100508689 5098 5103
1828 | 4272836 Disease DOID:216 15128 15141
1829 | 4272836 Disease DOID:216 15339 15352
1830 | 4272838 Gene 9847 26681 26685
1831 | 4272839 Gene 317 1781 1784
1832 | 4272839 Gene 317 3623 3626
1833 | 4272839 Gene 317 4577 4580
1834 | 4272839 Disease DOID:7148 5472 5513
1835 | 4272839 Gene 317 6267 6270
1836 | 4272839 Gene 317 7717 7720
1837 | 4272839 Disease DOID:1936 13782 13797
1838 | 4272839 Gene 5865 15902 15905
1839 | 4272839 Gene 317 29224 29227
1840 | 4272839 Gene 317 29451 29454
1841 | 4272839 Disease DOID:8398 32359 32373
1842 | 4272839 Gene 317 36822 36825
1843 | 4272840 Disease DOID:2531 51 67
1844 | 4272840 Disease DOID:2531 68 84
1845 | 4272840 Disease DOID:2531 212 219
1846 | 4272840 Disease DOID:2531 384 400
1847 | 4272840 Compound DB01042 484 493
1848 | 4272840 Compound DB01041 518 529
1849 | 4272840 Compound DB08889 580 591
1850 | 4272840 Disease DOID:2531 807 823
1851 | 4272840 Disease DOID:2531 922 938
1852 | 4272840 Disease DOID:2531 1197 1213
1853 | 4272840 Compound DB08889 1373 1384
1854 | 4272840 Compound DB08910 1386 1398
1855 | 4272840 Compound DB06317 1400 1410
1856 | 4272840 Compound DB06769 1412 1424
1857 | 4272840 Disease DOID:2531 1518 1535
1858 | 4272840 Disease DOID:2531 1886 1893
1859 | 4272840 Disease DOID:2531 1991 1998
1860 | 4272840 Disease DOID:2531 2052 2069
1861 | 4272840 Disease DOID:2531 2284 2291
1862 | 4272840 Disease DOID:2531 2372 2392
1863 | 4272840 Disease DOID:2531 2445 2452
1864 | 4272840 Disease DOID:2531 2663 2670
1865 | 4272840 Gene 4257 3367 3373
1866 | 4272840 Gene 4257 3513 3518
1867 | 4272840 Disease DOID:2531 3865 3889
1868 | 4272840 Disease DOID:2531 4669 4676
1869 | 4272840 Disease DOID:2531 4806 4822
1870 | 4272840 Disease DOID:2531 5478 5493
1871 | 4272840 Compound DB01042 5919 5928
1872 | 4272840 Compound DB00860 5934 5946
1873 | 4272840 Compound DB00635 7125 7135
1874 | 4272840 Compound DB01042 7617 7626
1875 | 4272840 Compound DB00635 7627 7637
1876 | 4272840 Compound DB01041 7638 7649
1877 | 4272840 Compound DB01041 7915 7926
1878 | 4272840 Compound DB01041 8368 8379
1879 | 4272840 Compound DB00531 8478 8494
1880 | 4272840 Compound DB01234 8499 8512
1881 | 4272840 Compound DB01041 8745 8756
1882 | 4272840 Disease DOID:2531 8886 8893
1883 | 4272840 Disease DOID:2531 8934 8950
1884 | 4272840 Compound DB01234 9013 9025
1885 | 4272840 Compound DB01234 9065 9077
1886 | 4272840 Disease DOID:2531 9104 9120
1887 | 4272840 Disease DOID:2531 9436 9443
1888 | 4272840 Compound DB01042 9712 9721
1889 | 4272840 Compound DB00635 9722 9732
1890 | 4272840 Compound DB00188 10329 10339
1891 | 4272840 Compound DB00188 10603 10613
1892 | 4272840 Compound DB00635 10627 10637
1893 | 4272840 Compound DB01042 10691 10700
1894 | 4272840 Compound DB01041 10720 10731
1895 | 4272840 Disease DOID:2531 10937 10953
1896 | 4272840 Compound DB00188 10975 10985
1897 | 4272840 Compound DB00188 11112 11122
1898 | 4272840 Disease DOID:2531 11256 11272
1899 | 4272840 Compound DB01041 11290 11301
1900 | 4272840 Compound DB00188 11507 11517
1901 | 4272840 Disease DOID:2531 12422 12438
1902 | 4272840 Compound DB00188 12577 12587
1903 | 4272840 Compound DB01041 12857 12868
1904 | 4272840 Disease DOID:2531 13543 13559
1905 | 4272840 Disease DOID:2531 13635 13651
1906 | 4272840 Disease DOID:2531 13716 13723
1907 | 4272840 Disease DOID:2531 13739 13755
1908 | 4272840 Disease DOID:2531 13883 13890
1909 | 4272840 Disease DOID:2531 13990 13997
1910 | 4272840 Disease DOID:2531 14258 14274
1911 | 4272840 Disease DOID:2531 14533 14549
1912 | 4272840 Compound DB08889 14709 14720
1913 | 4272840 Compound DB08910 14722 14734
1914 | 4272840 Compound DB06317 14736 14746
1915 | 4272840 Compound DB06769 14748 14760
1916 | 4272840 Disease DOID:2531 14902 14918
1917 | 4272840 Disease DOID:2531 14951 14967
1918 | 4272840 Disease DOID:2531 14968 14984
1919 | 4272840 Disease DOID:2531 15018 15034
1920 | 4272840 Disease DOID:2531 15124 15131
1921 | 4272840 Disease DOID:2531 15165 15181
1922 | 4272840 Disease DOID:2531 15196 15211
1923 | 4272840 Disease DOID:2531 15246 15262
1924 | 4272840 Disease DOID:2531 15375 15382
1925 | 4272840 Disease DOID:2531 15401 15416
1926 | 4272840 Disease DOID:2531 15459 15474
1927 | 4272840 Disease DOID:2531 15567 15574
1928 | 4272840 Disease DOID:2531 15647 15654
1929 | 4272840 Disease DOID:2531 15744 15760
1930 | 4272840 Disease DOID:2531 15806 15813
1931 | 4272840 Disease DOID:2531 15859 15875
1932 | 4272840 Disease DOID:2531 15948 15955
1933 | 4272840 Disease DOID:2531 16024 16031
1934 | 4272840 Disease DOID:2531 16062 16069
1935 | 4272840 Disease DOID:2531 16128 16144
1936 | 4272840 Disease DOID:2531 16216 16223
1937 | 4272840 Disease DOID:2531 16282 16289
1938 | 4272840 Disease DOID:2531 16324 16340
1939 | 4272840 Disease DOID:2531 16410 16426
1940 | 4272840 Disease DOID:2531 16476 16492
1941 | 4272840 Disease DOID:2531 16542 16558
1942 | 4272840 Disease DOID:2531 16559 16566
1943 | 4272840 Compound DB01042 16629 16638
1944 | 4272840 Compound DB00635 16644 16654
1945 | 4272840 Disease DOID:2531 16672 16688
1946 | 4272840 Compound DB01042 16746 16755
1947 | 4272840 Compound DB00635 16760 16770
1948 | 4272840 Compound DB01041 16776 16787
1949 | 4272840 Compound DB01042 16795 16804
1950 | 4272840 Compound DB00635 16809 16819
1951 | 4272840 Disease DOID:2531 16909 16925
1952 | 4272840 Compound DB01042 16970 16979
1953 | 4272840 Compound DB00635 16984 16994
1954 | 4272840 Compound DB01041 17000 17011
1955 | 4272840 Disease DOID:2531 17065 17081
1956 | 4272840 Compound DB01041 17110 17121
1957 | 4272840 Compound DB01042 17130 17139
1958 | 4272840 Compound DB00635 17140 17150
1959 | 4272840 Disease DOID:2531 17168 17184
1960 | 4272840 Disease DOID:2531 17265 17272
1961 | 4272840 Compound DB01042 17285 17294
1962 | 4272840 Compound DB00635 17299 17309
1963 | 4272840 Compound DB01041 17315 17326
1964 | 4272840 Disease DOID:2531 17363 17379
1965 | 4272840 Compound DB01041 17412 17423
1966 | 4272840 Compound DB01042 17433 17442
1967 | 4272840 Compound DB00635 17448 17458
1968 | 4272840 Disease DOID:2531 17500 17516
1969 | 4272840 Compound DB01042 17542 17551
1970 | 4272840 Compound DB00635 17553 17563
1971 | 4272840 Compound DB01041 17569 17580
1972 | 4272840 Disease DOID:2531 17606 17622
1973 | 4272840 Compound DB01041 17682 17693
1974 | 4272840 Disease DOID:2531 17721 17728
1975 | 4272840 Compound DB00531 17813 17829
1976 | 4272840 Compound DB01041 17831 17842
1977 | 4272840 Disease DOID:2531 17904 17920
1978 | 4272840 Compound DB01234 18039 18052
1979 | 4272840 Disease DOID:2531 18092 18108
1980 | 4272840 Disease DOID:2531 18220 18227
1981 | 4272840 Disease DOID:2531 18282 18298
1982 | 4272840 Compound DB00635 18329 18339
1983 | 4272840 Disease DOID:2531 18365 18381
1984 | 4272840 Compound DB00635 18412 18422
1985 | 4272840 Compound DB01042 18437 18446
1986 | 4272840 Compound DB00635 18451 18461
1987 | 4272840 Disease DOID:2531 18476 18503
1988 | 4272840 Compound DB00188 18580 18590
1989 | 4272840 Compound DB01042 18592 18601
1990 | 4272840 Compound DB00635 18607 18617
1991 | 4272840 Compound DB00188 18626 18636
1992 | 4272840 Compound DB01041 18638 18649
1993 | 4272840 Compound DB00635 18655 18665
1994 | 4272840 Compound DB00188 18726 18736
1995 | 4272840 Compound DB01041 18741 18752
1996 | 4272840 Compound DB00188 18760 18770
1997 | 4272840 Compound DB00635 18775 18785
1998 | 4272840 Disease DOID:2531 18821 18837
1999 | 4272840 Compound DB00188 18858 18868
2000 | 4272840 Compound DB00188 18968 18978
2001 | 4272840 Compound DB01042 18979 18988
2002 | 4272840 Compound DB00635 18989 18999
2003 | 4272840 Disease DOID:2531 19025 19041
2004 | 4272840 Compound DB00188 19109 19119
2005 | 4272840 Disease DOID:2531 19123 19139
2006 | 4272840 Disease DOID:2531 19202 19209
2007 | 4272841 Gene 4598 812 815
2008 | 4272841 Gene 9230 3250 3254
2009 | 4272842 Compound DB00882 3581 3599
2010 | 4272842 Compound DB00783 4204 4213
2011 | 4272842 Compound DB00396 4218 4230
2012 | 4272844 Gene 4363 815 818
2013 | 4272844 Gene 4363 908 911
2014 | 4272844 Gene 4363 1029 1032
2015 | 4272844 Gene 4363 1201 1204
2016 | 4272844 Gene 4363 1353 1356
2017 | 4272844 Gene 4363 1475 1478
2018 | 4272844 Gene 4363 1592 1595
2019 | 4272844 Gene 4363 4978 4981
2020 | 4272844 Gene 4363 5148 5151
2021 | 4272844 Gene 4363 5320 5323
2022 | 4272844 Gene 4363 5492 5495
2023 | 4272844 Gene 4363 5644 5647
2024 | 4272844 Gene 4363 5788 5791
2025 | 4272844 Gene 4363 6009 6012
2026 | 4272844 Gene 4363 6159 6162
2027 | 4272844 Gene 4363 6428 6431
2028 | 4272844 Gene 4363 6458 6461
2029 | 4272844 Gene 4363 6593 6596
2030 | 4272844 Gene 4363 6642 6645
2031 | 4272844 Gene 4363 6765 6768
2032 | 4272844 Gene 4363 6918 6921
2033 | 4272844 Gene 4363 6974 6977
2034 | 4272844 Gene 4363 7102 7105
2035 | 4272844 Gene 4363 7244 7247
2036 | 4272844 Gene 4363 7315 7318
2037 | 4272844 Gene 4363 7438 7441
2038 | 4272844 Gene 4363 7587 7590
2039 | 4272844 Gene 4363 8969 8972
2040 | 4272844 Gene 4363 9033 9036
2041 | 4272844 Gene 4363 9129 9132
2042 | 4272844 Gene 4363 9204 9207
2043 | 4272844 Gene 4363 9438 9441
2044 | 4272844 Gene 4363 9468 9471
2045 | 4272844 Gene 4363 9552 9555
2046 | 4272844 Gene 4363 9640 9643
2047 | 4272844 Gene 4363 9931 9934
2048 | 4272844 Gene 4363 9969 9972
2049 | 4272844 Gene 4363 10268 10271
2050 | 4272844 Gene 4363 10796 10799
2051 | 4272845 Disease DOID:784 1778 1799
2052 | 4272845 Disease DOID:784 2031 2052
2053 | 4272845 Disease DOID:784 3208 3229
2054 | 4272845 Disease DOID:784 5092 5114
2055 | 4272845 Compound DB03904 8315 8319
2056 | 4272845 Compound DB03904 8670 8674
2057 | 4272845 Disease DOID:10763 12090 12102
2058 | 4272845 Disease DOID:784 13657 13678
2059 | 4272845 Disease DOID:784 14019 14040
2060 | 4272845 Disease DOID:10763 14235 14247
2061 | 4272845 Disease DOID:10763 14476 14488
2062 | 4272846 Disease DOID:2531 6177 6194
2063 | 4272846 Gene 3055 8039 8042
2064 | 4272846 Disease DOID:14330 8754 8774
2065 | 4272846 Disease DOID:14330 9650 9670
2066 | 4272846 Disease DOID:7148 11722 11759
2067 | 4272846 Disease DOID:7147 11764 11786
2068 | 4272846 Disease DOID:263 13013 13031
2069 | 4272846 Disease DOID:184 13035 13054
2070 | 4272846 Disease DOID:7147 16840 16862
2071 | 4272846 Disease DOID:7147 17876 17898
2072 | 4272847 Disease DOID:3083 24 61
2073 | 4272847 Disease DOID:3083 166 203
2074 | 4272847 Disease DOID:3083 300 337
2075 | 4272847 Disease DOID:3083 1526 1563
2076 | 4272847 Disease DOID:2841 3208 3214
2077 | 4272847 Disease DOID:3083 3997 4034
2078 | 4272847 Compound DB00184 5519 5527
2079 | 4272847 Compound DB00184 5717 5725
2080 | 4272847 Disease DOID:10763 7983 7995
2081 | 4272847 Disease DOID:10763 8161 8173
2082 | 4272847 Disease DOID:3083 17830 17862
2083 | 4272847 Disease DOID:3083 17978 18015
2084 | 4272847 Compound DB00184 18405 18413
2085 | 4272847 Disease DOID:3083 18889 18926
2086 | 4272847 Disease DOID:3083 19138 19150
2087 | 4272847 Disease DOID:3083 19224 19261
2088 | 4272847 Disease DOID:9352 19551 19576
2089 | 4272847 Disease DOID:3083 19634 19671
2090 | 4272847 Disease DOID:3083 19760 19797
2091 |
--------------------------------------------------------------------------------
/data/example/README.md:
--------------------------------------------------------------------------------
1 | # Converting Pubtator Annotations to BioC XML
2 |
3 | This folder conatins two scirpts one that will convert [pubtator to bioC xml](pubtator_to_xml.py) and the other will [extract annoations](extract_tags.py) for snorkel to use.
4 |
5 | To run the pubtator converter use the following command:
6 |
7 | ```
8 | python ../../scripts/pubtator_to_xml.py --documents 1-sample-annotations.txt --output 2-sample-docs.xml
9 | ```
10 |
11 | To extract annotations from the BioC format use the following command:
12 | ```
13 | python ../../scripts/extract_tags.py --input 2-sample-docs.xml --output 3-sample-tags.tsv
14 | ```
15 |
--------------------------------------------------------------------------------
/data/example/ncbi_pmid_to_pmcid_map.tsv.xz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/greenelab/pubtator/4a7d7bcce1854ea338aca2256b0125f35b79b010/data/example/ncbi_pmid_to_pmcid_map.tsv.xz
--------------------------------------------------------------------------------
/data/temp/batch_log.tsv:
--------------------------------------------------------------------------------
1 | batch pmcid
2 | 0 PMC2289422
3 | 0 PMC2289423
4 | 0 PMC2289424
5 | 0 PMC2289425
6 | 0 PMC2289426
7 | 0 PMC2289427
8 | 0 PMC2289428
9 | 0 PMC2289429
10 | 0 PMC2289430
11 | 0 PMC2289434
12 | 0 PMC2289435
13 | 0 PMC2289436
14 | 0 PMC2289437
15 | 0 PMC2289438
16 | 0 PMC2289439
17 | 0 PMC2289440
18 | 0 PMC2289441
19 | 0 PMC2289442
20 | 0 PMC2289443
21 | 0 PMC2289444
22 | 0 PMC2289445
23 | 0 PMC2289446
24 | 0 PMC2289447
25 | 0 PMC2289448
26 | 0 PMC2289449
27 | 0 PMC2289450
28 | 0 PMC2289451
29 | 0 PMC2289452
30 | 0 PMC2289453
31 | 0 PMC2289454
32 | 0 PMC2289455
33 | 0 PMC2289456
34 | 0 PMC2289457
35 | 0 PMC2289458
36 | 0 PMC2289459
37 | 0 PMC2289460
38 | 0 PMC2289461
39 | 0 PMC2289462
40 | 0 PMC2289463
41 | 0 PMC2289464
42 | 0 PMC2289465
43 | 0 PMC2289466
44 | 0 PMC2289467
45 | 0 PMC2289468
46 | 0 PMC2289469
47 | 0 PMC2289470
48 | 0 PMC2289471
49 | 0 PMC2289472
50 | 0 PMC2289473
51 | 0 PMC2289474
52 | 0 PMC2289475
53 | 0 PMC2289476
54 | 0 PMC2289477
55 | 0 PMC2289478
56 | 0 PMC2289479
57 | 0 PMC2289480
58 | 0 PMC2289481
59 | 0 PMC2289482
60 | 0 PMC2289483
61 | 0 PMC2289484
62 | 0 PMC2289485
63 | 0 PMC2289486
64 | 0 PMC2289487
65 | 0 PMC2289488
66 | 0 PMC2289489
67 | 0 PMC2289490
68 | 0 PMC2289491
69 | 0 PMC2289492
70 | 0 PMC2289493
71 | 0 PMC2289494
72 | 0 PMC2289495
73 | 0 PMC2289496
74 | 0 PMC2289497
75 | 0 PMC2289498
76 | 0 PMC2289499
77 | 0 PMC2289500
78 | 0 PMC2289501
79 | 0 PMC2289502
80 | 0 PMC2289503
81 | 0 PMC2289504
82 | 0 PMC2289505
83 | 0 PMC2289506
84 | 0 PMC2289507
85 | 0 PMC2289508
86 | 0 PMC2289509
87 | 0 PMC2289510
88 | 0 PMC2289512
89 | 0 PMC2289513
90 | 0 PMC2289514
91 | 0 PMC2289515
92 | 0 PMC2289517
93 | 0 PMC2289518
94 | 0 PMC2289519
95 | 0 PMC2289520
96 | 0 PMC2289521
97 | 0 PMC2289522
98 | 0 PMC2289524
99 | 0 PMC2289525
100 | 0 PMC4272812
101 | 0 PMC4272813
102 | 1 PMC4272814
103 | 1 PMC4272815
104 | 1 PMC4272816
105 | 1 PMC4272818
106 | 1 PMC4272820
107 | 1 PMC4272821
108 | 1 PMC4272822
109 | 1 PMC4272823
110 | 1 PMC4272824
111 | 1 PMC4272825
112 | 1 PMC4272826
113 | 1 PMC4272827
114 | 1 PMC4272828
115 | 1 PMC4272829
116 | 1 PMC4272830
117 | 1 PMC4272831
118 | 1 PMC4272832
119 | 1 PMC4272833
120 | 1 PMC4272834
121 | 1 PMC4272835
122 | 1 PMC4272836
123 | 1 PMC4272837
124 | 1 PMC4272838
125 | 1 PMC4272839
126 | 1 PMC4272840
127 | 1 PMC4272841
128 | 1 PMC4272842
129 | 1 PMC4272843
130 | 1 PMC4272844
131 | 1 PMC4272845
132 | 1 PMC4272846
133 | 1 PMC4272847
134 |
--------------------------------------------------------------------------------
/download/bioconcepts2pubtator_offsets.gz.log:
--------------------------------------------------------------------------------
1 | --2017-02-16 18:49:50-- ftp://ftp.ncbi.nlm.nih.gov/pub/lu/PubTator/bioconcepts2pubtator_offsets.gz
2 | => ‘download/.listing’
3 | Resolving ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)... 2607:f220:41e:250::12, 130.14.250.12
4 | Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|2607:f220:41e:250::12|:21... connected.
5 | Logging in as anonymous ... Logged in!
6 | ==> SYST ... done. ==> PWD ... done.
7 | ==> TYPE I ... done. ==> CWD (1) /pub/lu/PubTator ... done.
8 | ==> EPSV ... done. ==> LIST ... done.
9 |
10 | 0K . 27.0K=0.05s
11 |
12 | 2017-02-16 18:49:51 (27.0 KB/s) - ‘download/.listing’ saved [1275]
13 |
14 | Removed ‘download/.listing’.
15 | Remote file no newer than local file ‘download/bioconcepts2pubtator_offsets.gz’ -- not retrieving.
16 |
--------------------------------------------------------------------------------
/execute.py:
--------------------------------------------------------------------------------
1 | import argparse
2 | from pathlib import Path
3 | import json
4 |
5 | import wget
6 |
7 | from scripts.download_full_text import download_full_text, merge_full_text
8 | from scripts.extract_tags import extract_annotations
9 | from scripts.hetnet_id_extractor import filter_tags
10 | from scripts.map_ids import map_ids
11 | from scripts.pubtator_to_xml import convert_pubtator
12 |
13 | parser = argparse.ArgumentParser(
14 | description='Runs Pubtator/Pubtator Central Parser Pipeline'
15 | )
16 |
17 | parser.add_argument(
18 | "--config", help="The config file for the extractor.",
19 | default="config_files/pubtator_central_config.json"
20 | )
21 |
22 | args = parser.parse_args()
23 |
24 | configuration = json.load(open(args.config, "r"))
25 |
26 | if (
27 | "repository_download" in configuration and
28 | not configuration["repository_download"]["skip"]
29 | ):
30 | print("Executing repository_download...")
31 | wget.download(
32 | configuration["repository_download"]['url'],
33 | out=configuration["repository_download"]['download_folder']
34 | )
35 |
36 | del configuration["repository_download"]
37 |
38 | if (
39 | "pubtator_to_xml" in configuration and
40 | not configuration["pubtator_to_xml"]["skip"]
41 | ):
42 | print("Executing pubtator_to_xml...")
43 | convert_pubtator(
44 | configuration["pubtator_to_xml"]['documents'],
45 | configuration["pubtator_to_xml"]['output']
46 | )
47 |
48 | del configuration["pubtator_to_xml"]
49 |
50 | if (
51 | "extract_tags" in configuration and
52 | not configuration["extract_tags"]["skip"]
53 | ):
54 | print("Executing extract_tags...")
55 | extract_annotations(
56 | configuration["extract_tags"]["input"],
57 | configuration["extract_tags"]["output"]
58 | )
59 |
60 | del configuration["extract_tags"]
61 |
62 | if (
63 | "hetnet_id_extractor" in configuration and
64 | not configuration["hetnet_id_extractor"]["skip"]
65 | ):
66 | print("Executing hetnet_id_extractor...")
67 | filter_tags(
68 | configuration["hetnet_id_extractor"]["input"],
69 | configuration["hetnet_id_extractor"]["output"]
70 | )
71 |
72 | del configuration["hetnet_id_extractor"]
73 |
74 | if (
75 | "map_pmids_to_pmcids" in configuration and
76 | not configuration["map_pmids_to_pmcids"]["skip"]
77 | ):
78 | print("Executing map_pmids_to_pmcids...")
79 | map_ids(
80 | configuration["map_pmids_to_pmcids"]["input"],
81 | configuration["map_pmids_to_pmcids"]["output"],
82 | configuration["map_pmids_to_pmcids"]["debug"]
83 | )
84 |
85 | del configuration["map_pmids_to_pmcids"]
86 |
87 | if (
88 | "download_full_text" in configuration and
89 | not configuration["download_full_text"]["skip"]
90 | ):
91 | print("Executing download_full_text...")
92 | download_full_text(
93 | configuration["download_full_text"]["input"],
94 | configuration["download_full_text"]["document_batch"],
95 | configuration["download_full_text"]["temp_dir"],
96 | configuration["download_full_text"]["log_file"]
97 | )
98 |
99 | merge_full_text(
100 | configuration["download_full_text"]["temp_dir"],
101 | configuration["download_full_text"]["output"]
102 | )
103 |
104 | del configuration["download_full_text"]
105 |
106 | if (
107 | "extract_full_text_tags" in configuration and
108 | not configuration["extract_full_text_tags"]["skip"]
109 | ):
110 | print("Executing extract_full_text_tags...")
111 | extract_annotations(
112 | configuration["extract_full_text_tags"]["input"],
113 | configuration["extract_full_text_tags"]["output"]
114 | )
115 |
116 | del configuration["extract_full_text_tags"]
117 |
118 | if (
119 | "hetnet_id_extractor_full_text" in configuration and
120 | not configuration["hetnet_id_extractor_full_text"]["skip"]
121 | ):
122 | print("Executing hetnet_id_extractor_full_text...")
123 | filter_tags(
124 | configuration["hetnet_id_extractor_full_text"]["input"],
125 | configuration["hetnet_id_extractor_full_text"]["output"]
126 | )
127 |
128 | del configuration["hetnet_id_extractor_full_text"]
129 |
130 | if len(configuration) > 0:
131 | not_executed_commands = '\n'.join(configuration.keys())
132 | print(
133 | "\n"
134 | "Commands not executed:\n"
135 | f"{not_executed_commands}"
136 | )
137 |
--------------------------------------------------------------------------------
/mapper/map_to_drugbank.py:
--------------------------------------------------------------------------------
1 | import pandas as pd
2 |
3 | # Map from DrugBank to MeSH using DrugCentral
4 | url = 'https://github.com/olegursu/drugtarget/blob/9a6d84bed8650c6c507a2d3d786814c774568610/identifiers.tsv?raw=true'
5 | drug_map_df = pd.read_table(url)
6 |
7 | drug_bank_df = drug_map_df[drug_map_df.ID_TYPE == 'DRUGBANK_ID'].rename(columns={"IDENTIFIER": "drugbank_id"})
8 | mesh_map_df = drug_map_df[drug_map_df.ID_TYPE.str.contains('MESH')].rename(columns={"IDENTIFIER": "identifier"})
9 | drug_bank_mesh_df = pd.merge(drug_bank_df[["DRUG_ID", "drugbank_id"]], mesh_map_df[["DRUG_ID", "identifier"]], on="DRUG_ID")
10 | drug_bank_mesh_df["source"] = "MESH"
11 | drug_bank_mesh_df = drug_bank_mesh_df.rename({})
12 |
13 | # Grab the chebi to DB mapper
14 | url = 'https://raw.githubusercontent.com/dhimmel/drugbank/7b94454b14a2fa4bb9387cb3b4b9924619cfbd3e/data/mapping/chebi.tsv'
15 | chebi_map_df = pd.read_table(url)
16 | chebi_map_df["chebi_id"] = chebi_map_df["chebi_id"].astype(object)
17 | chebi_map_df = chebi_map_df.rename(columns={"chebi_id": "identifier"})
18 | chebi_map_df["source"] = "CHEBI"
19 |
20 | final_df = drug_bank_mesh_df[["drugbank_id", "identifier", "source"]].append(chebi_map_df)
21 | final_df.to_csv("mapper/drugbank_mapper.tsv", sep="\t", index=False)
22 |
--------------------------------------------------------------------------------
/requirements.txt:
--------------------------------------------------------------------------------
1 | lxml==4.5.2
2 | pandas==0.25.3
3 | ratelimit==2.2.1
4 | requests==2.22.0
5 | tqdm==4.11.2
6 | wget==3.2
7 | numpy==1.23.1
8 | git+https://github.com/en-dash/PyBioC@a21bd181ce3b89de791db4bb7db6ca1c48167648
9 |
--------------------------------------------------------------------------------
/scripts/__init__.py:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/greenelab/pubtator/4a7d7bcce1854ea338aca2256b0125f35b79b010/scripts/__init__.py
--------------------------------------------------------------------------------
/scripts/download_full_text.py:
--------------------------------------------------------------------------------
1 | import argparse
2 | from pathlib import Path
3 | import requests
4 | import time
5 | import os
6 | import sys
7 |
8 | import lxml.etree as ET
9 | from lxml.etree import XMLSyntaxError
10 | import pandas as pd
11 | from ratelimit import limits, sleep_and_retry
12 | import tqdm
13 |
14 |
15 | QUERY_RATE = 60*15
16 | @sleep_and_retry
17 | @limits(calls=10000, period=QUERY_RATE)
18 | def call_api(url):
19 | response = requests.get(url)
20 |
21 | if response.status_code != 200:
22 | raise Exception(response.text)
23 |
24 | return response
25 |
26 | def read_id_chunk(id_file, batch_size):
27 | """
28 | Chunk the pandas dataframe so not everything is read into memory
29 |
30 | Keyword Arguments:
31 | id_file -- the file to read through pandas
32 | batch_size -- the size of each chunk
33 | """
34 | for id_batch in pd.read_csv(id_file, sep="\t", chunksize=batch_size):
35 | yield id_batch
36 |
37 | def download_full_text(ids_file, document_batch, temp_dir, log_file="batch_log.tsv"):
38 | """
39 | Download full text from Pubtator Central.
40 | This section involves heavy api calls and subject to get blocked.
41 | Email the researchers at pubtator if this script continues to be blocked
42 |
43 | Keywords arguments:
44 | ids_file -- The path containing the pmids to pmcids map
45 | document_batch -- the size of each id batch
46 | temp_dir -- the directory to hold full text batches from pubtator central api
47 | """
48 |
49 | # Pubtator supports biocxml and json
50 | # This script only uses biocxml
51 | pubtator_central_api = "https://www.ncbi.nlm.nih.gov/research/pubtator-api/publications/export/biocxml?"
52 |
53 | # Create the directory if it doesn't exist
54 | Path(f"{temp_dir}").mkdir(parents=True, exist_ok=True)
55 |
56 | # Load a logger to track which ids have been queried
57 | log_file_path = Path(f"{temp_dir}/{log_file}")
58 | if not log_file_path.exists():
59 | log = pd.DataFrame([], columns=["batch", "pmcid"])
60 | log.to_csv(
61 | log_file_path.resolve(),
62 | sep="\t", index=False
63 | )
64 |
65 | else:
66 | log = pd.read_csv(
67 | log_file_path.resolve(),
68 | sep="\t"
69 | )
70 |
71 | # test each query against Pubtator's API
72 | for idx, pmcid_batch_df in tqdm.tqdm(enumerate(read_id_chunk(ids_file, document_batch))):
73 |
74 | # Measure the ids that haven't been seen by the logger
75 | already_seen = (
76 | set(pmcid_batch_df.PMCID.values)
77 | .difference(set(log.pmcid.values))
78 | )
79 |
80 | # If all ids have been processed skip batch
81 | if len(already_seen) == 0:
82 | continue
83 |
84 | query = f"{pubtator_central_api}pmcids={','.join(pmcid_batch_df.PMCID.values)}"
85 | response = call_api(query)
86 |
87 | batch_file_path = Path(f"{temp_dir}/batch_{idx}.xml")
88 | with open(batch_file_path.resolve(), "wb") as xml_file:
89 | try:
90 | root = ET.fromstring(
91 | bytes(response.text, encoding="utf8")
92 | )
93 |
94 | xml_file.write(ET.tostring(root, pretty_print=True))
95 |
96 | # Save to the logger each pmcid batch
97 | (
98 | log
99 | .assign(
100 | batch=[idx]*pmcid_batch_df.shape[0],
101 | pmcid=pmcid_batch_df.PMCID.values.tolist()
102 | )
103 | .to_csv(
104 | f"{temp_dir}/{log_file}", sep="\t",
105 | mode="a", header=False, index=False
106 | )
107 | )
108 |
109 | except Exception as e:
110 | sys.stderr.write(
111 | f"There is an error processing batch {idx}."
112 | )
113 |
114 | sys.stderr.write(
115 | f"Here is the query:{query}."
116 | )
117 |
118 |
119 | def merge_full_text(temp_dir, output):
120 | """
121 | Download full text from Pubtator Central.
122 | This section involves heavy api calls and subject to get blocked.
123 | Email the researchers at pubtator if this script continues to be blocked
124 |
125 | Keywords arguments:
126 | temp_dir -- The path containing the pmids to pmcids map
127 | output -- the size of each id batch
128 | """
129 | batch_files = Path().rglob(f"{temp_dir}/*.xml")
130 |
131 | with open(output, "wb") as xml_file:
132 | first_file = True
133 |
134 | for file in tqdm.tqdm(batch_files):
135 | try:
136 | tree = ET.parse(str(file.resolve()))
137 | root = tree.getroot()
138 |
139 | # Write Header for output
140 | if first_file:
141 | # write opening tag to file
142 | xml_file.write(b"\n")
143 |
144 | for tag in root.getchildren():
145 | if tag.tag == "date":
146 | tag.text = time.strftime("%Y/%m/%d")
147 |
148 | # skip document tags will incorporate later
149 | if tag.tag == "document":
150 | break
151 |
152 | xml_file.write(ET.tostring(tag, pretty_print=True))
153 |
154 | first_file = False
155 |
156 | for document in root.xpath("document"):
157 | xml_file.write(ET.tostring(document, pretty_print=True))
158 |
159 | except XMLSyntaxError as e:
160 | sys.stderr.write(
161 | f"Please check {file}! There is an error at: {e}",
162 | )
163 |
164 | sys.stderr.write(
165 | "I am skipping this file.",
166 | )
167 |
168 | xml_file.write(b"\n")
169 |
170 | if __name__ == '__main__':
171 | parser = argparse.ArgumentParser(description='Extracts the annotations from the BioC xml format')
172 | parser.add_argument("--input", help="a tsv file that contains pmids to query for full text", required=True)
173 | parser.add_argument("--document_batch", help="the number of documents to query at once", default=100, type=int)
174 | parser.add_argument("--temp_dir", help="The directory to store the temporary files", required=True, type=str)
175 | parser.add_argument("--log_file", help="The directory to store the temporary files", default="batch_log.tsv", type=str)
176 | parser.add_argument("--output", help="the name of the outputfile containing full text documents", default="pubtator_full_text.xml")
177 | args = parser.parse_args()
178 |
179 | download_full_text(args.input, args.document_batch, args.temp_dir, args.log_file)
180 | merge_full_text(args.temp_dir, args.output)
181 |
--------------------------------------------------------------------------------
/scripts/extract_tags.py:
--------------------------------------------------------------------------------
1 | import argparse
2 | import csv
3 | import re
4 |
5 | from lxml import etree as ET
6 | import tqdm
7 |
8 | import scripts.utilities as utilities
9 |
10 |
11 |
12 | def extract_annotations(xml_path, tsv_path):
13 | """
14 | Extract the annotations from pubtator xml formatted file
15 | Outputs a TSV file with the following header terms:
16 | Document - the corresponding pubmed id
17 | Type - the type of term (i.e. Chemical, Disease, Gene etc.)
18 | ID - the appropiate MESH or NCBI ID if known
19 | Offset - the character position where the term starts
20 | End - the character position where the term ends
21 |
22 | Keywords arguments:
23 | xml_path -- The path to the xml data file
24 | tsv_path -- the path to output the formatted data
25 | """
26 | xml_opener = utilities.get_opener(xml_path)
27 | csv_opener = utilities.get_opener(tsv_path)
28 | with xml_opener(xml_path, "rb") as xml_file, csv_opener(tsv_path, "wt") as tsv_file:
29 | fieldnames = ['pubmed_id', 'type', 'identifier', 'offset', 'end']
30 | writer = csv.DictWriter(tsv_file, fieldnames=fieldnames, delimiter='\t')
31 | writer.writeheader()
32 | tag_generator = ET.iterparse(xml_file, tag="document", recover=True, encoding="utf-8")
33 |
34 | try:
35 | for event, document in tqdm.tqdm(tag_generator):
36 |
37 | pubmed_id = document[0].text
38 |
39 | # cycle through all the annotation tags contained within document tag
40 | for annotation in document.iter('annotation'):
41 |
42 | # not all annotations will contain an ID
43 | if len(annotation) <= 3:
44 | continue
45 |
46 | for infon in annotation.iter('infon'):
47 | if infon.attrib["key"] == "type":
48 | ant_type = infon.text
49 | else:
50 |
51 | if not infon.text:
52 | continue
53 |
54 | ant_id = re.sub("(MESH:|CVCL:)", "", str(infon.text))
55 |
56 | location, = annotation.iter('location')
57 | offset = int(location.attrib['offset'])
58 | end = offset + int(location.attrib['length'])
59 | row = {'pubmed_id': pubmed_id, 'type': ant_type, 'identifier': ant_id, 'offset': offset, 'end': end}
60 | writer.writerow(row)
61 |
62 | # prevent memory overload
63 | document.clear()
64 |
65 | except Exception as e:
66 | print(e)
67 | print(document[0].text)
68 |
69 | if __name__ == '__main__':
70 | parser = argparse.ArgumentParser(description='Export tags in a BioC XML file to a TSV table')
71 | parser.add_argument("--input", help="Path for the input BioC XML file", type=str, required=True)
72 | parser.add_argument("--output", nargs="?", help="Path for the output TSV file", required=True)
73 |
74 | args = parser.parse_args()
75 |
76 | extract_annotations(xml_path=args.input, tsv_path=args.output)
77 |
--------------------------------------------------------------------------------
/scripts/hetnet_id_extractor.py:
--------------------------------------------------------------------------------
1 | import argparse
2 |
3 | import pandas as pd
4 | import tqdm
5 |
6 | import scripts.utilities as utilities
7 |
8 | def filter_tags(infile, outfile):
9 | """ This method filters pubtator tags to consist of only
10 | hetnet tags
11 |
12 | Keyword arguments:
13 | infile -- the name of the file to read
14 | outfile -- the name of the output file
15 | """
16 |
17 | print_header = True
18 | hetnet_chemical_df = load_chemical_df()
19 | hetnet_disease_df = load_disease_df()
20 | hetnet_gene_df = load_gene_df()
21 | csv_opener = utilities.get_opener(outfile)
22 |
23 | with csv_opener(outfile, "wt") as tsv_file:
24 | for extracted_tag_df in tqdm.tqdm(get_tag_chunks(infile)):
25 |
26 | # Covert chemical IDs
27 | chemical_merged_df = (
28 | pd.merge(
29 | extracted_tag_df[extracted_tag_df["type"] == "Chemical"],
30 | hetnet_chemical_df[["drugbank_id", "identifier"]],
31 | left_on="identifier",
32 | right_on="identifier"
33 | )
34 | .drop_duplicates()
35 | .replace({"type":{"Chemical": "Compound"}})
36 | [["pubmed_id", "type", "offset", "end", "drugbank_id"]]
37 | .rename(columns={"drugbank_id": "identifier"})
38 | )
39 |
40 | # Convert Disease IDs
41 | disease_merged_df = (
42 | pd.merge(
43 | extracted_tag_df[extracted_tag_df["type"] == "Disease"],
44 | hetnet_disease_df[["doid_code", "resource_id"]],
45 | left_on="identifier",
46 | right_on="resource_id"
47 | )
48 | .drop_duplicates()
49 | [["pubmed_id", "type", "offset", "end", "doid_code"]]
50 | .rename(columns={"doid_code": "identifier"})
51 | )
52 |
53 | # Verify Gene IDs are human genes
54 | gene_df = extracted_tag_df[extracted_tag_df["type"] == "Gene"]
55 | gene_final_df = gene_df[gene_df["identifier"].isin(hetnet_gene_df["GeneID"])]
56 |
57 | final_df = (
58 | gene_final_df
59 | .append(chemical_merged_df, sort=True)
60 | .append(disease_merged_df, sort=True)
61 | )
62 |
63 | if print_header:
64 | (
65 | final_df
66 | [["pubmed_id", "type", "identifier", "offset", "end"]]
67 | .sort_values(["pubmed_id", "offset"])
68 | .to_csv(tsv_file, sep="\t", index=False)
69 | )
70 |
71 | print_header = False
72 | else:
73 | (
74 | final_df
75 | [["pubmed_id", "type", "identifier", "offset", "end"]]
76 | .sort_values(["pubmed_id", "offset"])
77 | .to_csv(tsv_file, sep="\t", index=False, header=False)
78 | )
79 |
80 |
81 | def get_tag_chunks(filename):
82 | """ Chunk the pandas dataframe so not everything is read into memory
83 |
84 | Keyword Arguments:
85 | filename -- the file to read through pandas
86 | """
87 | chunksize = 10 ** 6
88 | for chunk in pd.read_table(filename, chunksize=chunksize):
89 | yield chunk
90 |
91 |
92 | def load_disease_df():
93 | """
94 | Load the mesh-hetnet id mapping table.
95 | Return a dataframe of id mappings
96 | """
97 | url = 'https://raw.githubusercontent.com/dhimmel/disease-ontology/052ffcc960f5897a0575f5feff904ca84b7d2c1d/data/xrefs-prop-slim.tsv'
98 | disease_df = pd.read_table(url)
99 | return disease_df[disease_df["resource"] == "MSH"]
100 |
101 |
102 | def load_chemical_df():
103 | """
104 | Loads the chebi-mesh-drugbank id mapping table
105 | Return a dataframe with id mappings
106 | """
107 | return pd.read_table("mapper/drugbank_mapper.tsv")
108 |
109 |
110 | def load_gene_df():
111 | """
112 | Loads the gene table from hetnets
113 | Return a dataframe with the gene ids
114 | """
115 | url = 'https://raw.githubusercontent.com/dhimmel/entrez-gene/a7362748a34211e5df6f2d185bb3246279760546/data/genes-human.tsv'
116 | gene_df = pd.read_table(url).astype({"GeneID": str})
117 | return gene_df[gene_df["type_of_gene"] == "protein-coding"]
118 |
119 | if __name__ == '__main__':
120 | parser = argparse.ArgumentParser(description='Filter extracted tags to contain Hetnet IDs in a TSV table')
121 | parser.add_argument("--input", help="Path for the tsv tag table", type=str, required=True)
122 | parser.add_argument("--output", nargs="?", help="Path for the output TSV file", type=str, required=True)
123 |
124 | args = parser.parse_args()
125 |
126 | filter_tags(infile=args.input, outfile=args.output)
127 |
--------------------------------------------------------------------------------
/scripts/map_ids.py:
--------------------------------------------------------------------------------
1 | import argparse
2 | import requests
3 |
4 | import lxml.etree as ET
5 | import pandas as pd
6 | import tqdm
7 |
8 | def read_tag_chunks(id_file, batch_size):
9 | """
10 | Chunk the pandas dataframe so not everything is read into memory
11 |
12 | Keyword Arguments:
13 | id_file -- the file to read through pandas
14 | batch_size -- the size of each chunk
15 | """
16 | for pmids_df in pd.read_csv(id_file, chunksize=batch_size, sep="\t"):
17 | yield (
18 | pmids_df
19 | .drop_duplicates('pubmed_id')
20 | .rename(index=str, columns={"pubmed_id":"PMID"})
21 | .astype({"PMID":str})
22 | )
23 |
24 | def map_ids(ids_file, id_output, debug):
25 | """
26 | Extracts pmids from pubtator and then attempts to map pmids to pmcids
27 | This section is subject to be blocked since it relies on api calls.
28 | If this script continues to be blocked please email the researchers at pubtator
29 |
30 | Outputs a TSV file with the following header terms:
31 | pubmed_id - the corresponding pubmed id
32 | pmcids - the corresponding pubmed central ids
33 |
34 | Keywords arguments:
35 | ids_file -- The path to the extracted tag file
36 | email -- email to be reached at
37 | id_batch -- the id batch to query pubmed central from
38 | id_output --- the file name for the mapped ids
39 | """
40 | if debug:
41 | pmids_to_pmcids = pd.read_csv(
42 | "data/example/ncbi_pmid_to_pmcid_map.tsv.xz",
43 | dtype={
44 | "PMID": str,
45 | "Year": int,
46 | "Issue":str
47 | },
48 | sep="\t"
49 | )
50 | else:
51 | pmids_to_pmcids = pd.read_csv(
52 | "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/PMC-ids.csv.gz",
53 | dtype={
54 | "PMID": str,
55 | "Year": int,
56 | "Issue":str
57 | }
58 | )
59 |
60 | pmcid_batch = []
61 | for pmids_df in tqdm.tqdm(read_tag_chunks(ids_file, 1e6)):
62 | mapped_ids = pmids_to_pmcids.merge(pmids_df[["PMID"]], on="PMID")
63 |
64 | if not mapped_ids.empty:
65 | pmcid_batch.append(mapped_ids)
66 |
67 |
68 | full_mapped_ids = pd.concat(pmcid_batch)
69 | (
70 | full_mapped_ids
71 | .drop_duplicates()
72 | .to_csv(f"{id_output}", sep="\t", index=False)
73 | )
74 |
75 | if __name__ == '__main__':
76 | parser = argparse.ArgumentParser(description='Extracts the annotations from the BioC xml format')
77 | parser.add_argument("--input", help="a tsv file that contains pmids to merge with pmcids list", required=True)
78 | parser.add_argument("--output", help="the name of the output file that contains mapped ids", default="pmids_to_pmcids_map.tsv")
79 | parser.add_argument("--debug", help="this flag is used to pre-load ncbi's pmid to pmcid id table", action="store_true")
80 | args = parser.parse_args()
81 |
82 | map_ids(args.input, args.output, args.debug)
83 |
--------------------------------------------------------------------------------
/scripts/pubtator_to_xml.py:
--------------------------------------------------------------------------------
1 | import argparse
2 | import csv
3 | import os
4 | import re
5 | import time
6 |
7 | from bioc import BioCWriter, BioCCollection, BioCDocument, BioCPassage
8 | from bioc import BioCAnnotation, BioCLocation
9 | from itertools import groupby
10 | from lxml.builder import E
11 | from lxml.etree import tostring
12 | import tqdm
13 |
14 | import scripts.utilities as utilities
15 |
16 |
17 | def bioconcepts2pubtator_annotations(tag, index):
18 | """Bioconcepts to Annotations
19 | Specifically for bioconcepts2pubtator and converts each annotation
20 | into an annotation object that BioC can parse.
21 | Keyword Arguments:
22 | tag -- the annotation line that was parsed into an array
23 | index -- the id of each document specific annotation
24 | """
25 |
26 | annt = BioCAnnotation()
27 | annt.id = str(index)
28 | annt.infons["type"] = tag["type"]
29 |
30 | # If the annotation type is a Gene,Species, Mutation, SNP
31 | # Write out relevant tag
32 | tag_type = tag['type'] or ''
33 | tag_id = tag['tag_id']
34 | if tag_type == "Gene":
35 | annt.infons["NCBI Gene"] = tag_id
36 |
37 | elif tag_type == "Species":
38 | annt.infons["NCBI Species"] = tag_id
39 |
40 | elif "Mutation" in tag_type:
41 | annt.infons["tmVar"] = tag_id
42 |
43 | elif "SNP" in tag_type:
44 | annt.infons["tmVar"] = tag_id
45 |
46 | else:
47 | # If there is no MESH ID for an annotation
48 | if tag_id:
49 | # check to see if there are multiple mesh tags
50 | if "|" in tag_id:
51 | # Write out each MESH id as own tag
52 | for tag_num, ids in enumerate(tag_id.split("|")):
53 | # Some ids dont have the MESH:#### form so added case to that
54 | if ":" not in ids:
55 | annt.infons["MESH {}".format(tag_num)] = tag_id
56 | else:
57 | term_type, term_id = ids.split(":")
58 | annt.infons["{} {}".format(term_type, tag_num)] = term_id
59 | else:
60 | # Some ids dont have the MESH:#### form so added case to that
61 | if ":" in tag_id:
62 | term_type, term_id = tag_id.split(":")
63 | annt.infons[term_type] = term_id
64 | else:
65 | annt.infons["MESH"] = tag_id
66 | else:
67 | annt.infons["MESH"] = "Unknown"
68 |
69 | location = BioCLocation()
70 | location.offset = str(tag["start"])
71 | location.length = str(len(tag["term"]))
72 | annt.locations.append(location)
73 | annt.text = tag["term"]
74 | return annt
75 |
76 |
77 | def pubtator_stanza_to_article(lines):
78 | """Article Generator
79 | Returns an article that is a dictionary with the following keywords:
80 | pubmed_id - a document identifier
81 | Title- the title string
82 | Abstract- the abstract string
83 | Title_Annot- A filtered list of tags specific to the title
84 | Abstract_Annot- A filtered list of tags specific to the abstract
85 | Keywords:
86 | lines - this is a list of file lines passed from bioconcepts2pubtator_offsets function
87 | """
88 | article = {}
89 |
90 | # title
91 | title_heading = lines[0].split('|')
92 | article["pubmed_id"] = title_heading[0]
93 | article["title"] = title_heading[2]
94 | title_len = len(title_heading[2])
95 |
96 | # abstract
97 | abstract_heading = lines[1].split("|")
98 | article["abstract"] = abstract_heading[2]
99 |
100 | # Fix null characters
101 | fixed_lines = [
102 | str_with_null.replace('\x00', '')
103 | for str_with_null in lines[2:]
104 | ]
105 |
106 | # set up the csv reader
107 | annts = (
108 | csv.DictReader(
109 | fixed_lines,
110 | fieldnames=['pubmed_id', 'start', 'end', 'term', 'type', 'tag_id'],
111 | delimiter="\t",
112 | quoting=csv.QUOTE_NONE
113 | )
114 | )
115 |
116 | annts = list(annts)
117 |
118 | for annt in annts:
119 | for key in 'start', 'end':
120 | annt[key] = int(annt[key])
121 |
122 | annts.sort(key=lambda x: x["start"])
123 | article["title_annot"] = filter(lambda x: x["start"] < title_len, annts)
124 | article["abstract_annot"] = filter(lambda x: x["start"] > title_len, annts)
125 |
126 | return article
127 |
128 |
129 | def read_bioconcepts2pubtator_offsets(path):
130 | """Bioconcepts to pubtator
131 |
132 | Yields an article that is a dictionary described in the article generator
133 | function.
134 |
135 | Keywords:
136 | path - the path to the bioconcepts2putator_offset file (obtained from pubtator's ftp site: ftp://ftp.ncbi.nlm.nih.gov/pub/lu/PubTator/)
137 | """
138 | opener = utilities.get_opener(path)
139 | f = opener(path, "rt")
140 |
141 | lines = (line.rstrip() for line in f)
142 |
143 | for k, g in groupby(lines, key=bool):
144 | # Group articles based on empty lines as separators. Only pass
145 | # on non-empty lines.
146 | g = list(g)
147 | if g[0]:
148 | yield pubtator_stanza_to_article(g)
149 |
150 | f.close()
151 |
152 |
153 | def convert_pubtator(input_path, output_path):
154 | """Convert pubtators annotation list to BioC XML
155 | Keyword Arguments:
156 | input_file -- the path of pubtators annotation file
157 | output_file -- the path to output the BioC XML file
158 | """
159 |
160 | # Set up BioCWriter to write specifically Pubtator
161 | # Can change to incorporate other sources besides pubtator
162 | writer = BioCWriter()
163 | writer.collection = BioCCollection()
164 | collection = writer.collection
165 | collection.date = time.strftime("%Y/%m/%d")
166 | collection.source = "Pubtator"
167 | collection.key = "Pubtator.key"
168 |
169 | opener = utilities.get_opener(output_path)
170 | with opener(output_path, 'wb') as xml_file:
171 |
172 | # Have to manually do this because hangs otherwise
173 | # Write the head of the xml file
174 | xml_shell = writer.tostring('UTF-8')
175 | *xml_head, xml_tail = xml_shell.rstrip().split(b'\n')
176 | for line in xml_head:
177 | xml_file.write(line + b'\n')
178 |
179 | article_generator = read_bioconcepts2pubtator_offsets(input_path)
180 | # Write each article in BioC format
181 | for article in tqdm.tqdm(article_generator):
182 | try:
183 | # Skip the documents that have more than 1M characters
184 | # Pubtator contains sections that are large list of author
185 | # names which is why this check is needed
186 | if len(article['abstract']) > 1e5:
187 | continue
188 |
189 | document = BioCDocument()
190 | document.id = article["pubmed_id"]
191 |
192 | title_passage = BioCPassage()
193 | title_passage.put_infon('type', 'title')
194 | title_passage.offset = '0'
195 | title_passage.text = article["title"]
196 |
197 | abstract_passage = BioCPassage()
198 | abstract_passage.put_infon('type', 'abstract')
199 | abstract_passage.offset = str(len(article["title"]) + 1)
200 | abstract_passage.text = article["abstract"]
201 |
202 | id_index = 0
203 | for tag in article["title_annot"]:
204 | title_passage.annotations.append(bioconcepts2pubtator_annotations(tag, id_index))
205 | id_index += 1
206 |
207 | for tag in article["abstract_annot"]:
208 | abstract_passage.annotations.append(bioconcepts2pubtator_annotations(tag, id_index))
209 | id_index += 1
210 |
211 | document.add_passage(title_passage)
212 | document.add_passage(abstract_passage)
213 |
214 | step_parent = E('collection')
215 | writer._build_documents([document], step_parent)
216 | xml_file.write(tostring(step_parent[0], pretty_print=True))
217 | step_parent.clear()
218 |
219 | except Exception as e:
220 | print(e)
221 | print(f"Article that broke: {article['pubmed_id']}")
222 | step_parent.clear()
223 |
224 | # Write the closing tag of the xml document
225 | xml_file.write(xml_tail + b'\n')
226 |
227 |
228 | if __name__ == '__main__':
229 | parser = argparse.ArgumentParser(description='Extracts the annotations from the BioC xml format')
230 | parser.add_argument("--documents", help="Path pointing to input file.", required=True)
231 | parser.add_argument("--output", help="Path for destination of output.", required=True)
232 | args = parser.parse_args()
233 |
234 | convert_pubtator(args.documents, args.output)
235 |
--------------------------------------------------------------------------------
/scripts/utilities.py:
--------------------------------------------------------------------------------
1 | import mimetypes
2 | import importlib
3 |
4 | encoding_to_module = {
5 | 'gzip': 'gzip',
6 | 'bzip2': 'bz2',
7 | 'xz': 'lzma',
8 | }
9 |
10 | def get_opener(filename):
11 | """
12 | Automatically detect compression and return the file opening function.
13 | """
14 | type_, encoding = mimetypes.guess_type(filename)
15 | if encoding is None:
16 | opener = open
17 | else:
18 | module = encoding_to_module[encoding]
19 | opener = importlib.import_module(module).open
20 | return opener
21 |
--------------------------------------------------------------------------------
/tests.sh:
--------------------------------------------------------------------------------
1 | set -o errexit
2 |
3 | python execute.py \
4 | --config config_files/tests_config.json
5 |
--------------------------------------------------------------------------------