├── tests └── foo ├── src ├── example │ ├── iao.doc │ └── community-label.owl ├── tools │ ├── get-ontofox-imports │ ├── clean-ontofox-results.pl │ └── build │ │ ├── uri-report.lisp │ │ ├── iao.asd │ │ ├── external-templates.txt │ │ ├── write-purls.lisp │ │ ├── IAOTools │ │ └── src │ │ │ └── ca │ │ │ └── bccrc │ │ │ └── iao │ │ │ └── IAOIdUpdater.java │ │ └── modify-uris.pl └── ontology │ ├── ontoFox │ ├── RO_input.txt │ ├── UO_input.txt │ ├── PATO_input.txt │ └── OBI_input.txt │ ├── LICENSE │ ├── catalog-v001.xml │ ├── imports │ ├── import_RO.owl │ ├── externalByHand.owl │ ├── import_UO.owl │ └── import_PATO.owl │ └── template │ ├── IAO_synonyms.tsv │ └── IAO_newTerms.tsv ├── releases ├── 2012-01-05 │ ├── doc │ │ ├── qc.xlsx │ │ ├── termsMapping.xlsx │ │ ├── replaceIRIs.pl │ │ └── termsMapping.txt │ ├── ontology │ │ ├── catalog-v001.xml │ │ ├── IAO.owl │ │ └── external.owl │ ├── ontology_BFO2 │ │ ├── catalog-v001.xml │ │ ├── IAO.owl │ │ └── external.owl │ └── merged │ │ ├── iao.owl │ │ └── iao-inferredSuperClasses.owl ├── 2015-02-23 │ ├── release notes.docx │ ├── merged │ │ └── iao_inferredSuperClasses.owl │ └── ontology │ │ ├── externalByHand.owl │ │ └── IAO.owl ├── 2017-01-06 │ ├── make-release.lisp │ ├── purls.yml │ ├── catalog-v001.xml │ ├── release-notes.txt │ ├── ro │ │ └── bfo-axioms.owl │ └── externalByHand.owl ├── 2017-03-24 │ ├── make-release.lisp │ ├── purls.yml │ ├── release-notes.txt │ ├── catalog-v001.xml │ ├── ro │ │ └── bfo-axioms.owl │ └── externalByHand.owl ├── 2012-07-11-BFO2 │ ├── catalog-v001.xml │ └── IAO.owl ├── 2011-08-04 │ ├── ontology │ │ ├── catalog-v001.xml │ │ ├── IAO.owl │ │ └── external.owl │ └── merged │ │ └── iao.owl ├── 2009-11-02 │ ├── merged │ │ └── iao.owl │ └── ontology │ │ ├── IAO.owl │ │ └── external.owl ├── 2010-09-14 │ ├── iao.owl │ ├── external │ │ └── protege.owl │ └── external.owl ├── 2009-11-06 │ ├── merged │ │ └── iao.owl │ └── ontology │ │ ├── IAO.owl │ │ └── external.owl ├── 2010-10-26 │ ├── iao.owl │ └── external.owl └── 2011-05-09 │ ├── iao.owl │ ├── external │ └── protege.owl │ └── external.owl ├── docs ├── BFO 1.1 to 2.0 conversion │ ├── termsMapping.xlsx │ ├── notes.txt │ └── mapping.txt ├── issue attachment │ ├── issue76-ConceptualIssues.pdf │ ├── issue147-reddy_1979_conduit_metaphor.pdf │ └── issue34-Exception - URI Resolution Failure.pdf └── QC-report.csv ├── .github └── workflows │ └── qc.yml ├── CONTRIBUTING.md ├── Makefile └── README.md /tests/foo: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/example/iao.doc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/information-artifact-ontology/IAO/HEAD/src/example/iao.doc -------------------------------------------------------------------------------- /releases/2012-01-05/doc/qc.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/information-artifact-ontology/IAO/HEAD/releases/2012-01-05/doc/qc.xlsx -------------------------------------------------------------------------------- /releases/2015-02-23/release notes.docx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/information-artifact-ontology/IAO/HEAD/releases/2015-02-23/release notes.docx -------------------------------------------------------------------------------- /releases/2012-01-05/doc/termsMapping.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/information-artifact-ontology/IAO/HEAD/releases/2012-01-05/doc/termsMapping.xlsx -------------------------------------------------------------------------------- /docs/BFO 1.1 to 2.0 conversion/termsMapping.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/information-artifact-ontology/IAO/HEAD/docs/BFO 1.1 to 2.0 conversion/termsMapping.xlsx -------------------------------------------------------------------------------- /docs/issue attachment/issue76-ConceptualIssues.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/information-artifact-ontology/IAO/HEAD/docs/issue attachment/issue76-ConceptualIssues.pdf -------------------------------------------------------------------------------- /src/tools/get-ontofox-imports: -------------------------------------------------------------------------------- 1 | #!/bin/bash -x 2 | curl -s -F file=@OntoFox-input.txt http://ontofox.hegroup.org/service.php | perl clean-ontofox-results.pl > ../import-OBO.owl 3 | -------------------------------------------------------------------------------- /docs/issue attachment/issue147-reddy_1979_conduit_metaphor.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/information-artifact-ontology/IAO/HEAD/docs/issue attachment/issue147-reddy_1979_conduit_metaphor.pdf -------------------------------------------------------------------------------- /docs/issue attachment/issue34-Exception - URI Resolution Failure.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/information-artifact-ontology/IAO/HEAD/docs/issue attachment/issue34-Exception - URI Resolution Failure.pdf -------------------------------------------------------------------------------- /releases/2017-01-06/make-release.lisp: -------------------------------------------------------------------------------- 1 | Made with LSW https://github.com/alanruttenberg/lsw2/ 2 | Commit: 4f49e66a80c83fc6ec50523ce0494d76fabb577f 3 | 4 | (make-release "iao" "~/repos/information-artifact-ontology/src/ontology/iao.owl" 5 | :when 3692716953 6 | :additional-products '("ontology-metadata.owl" "iao-main")) 7 | -------------------------------------------------------------------------------- /releases/2017-03-24/make-release.lisp: -------------------------------------------------------------------------------- 1 | Made with LSW https://github.com/alanruttenberg/lsw2/ 2 | Commit: 220042aaab4b7b65c1291f6351cbfe9b9940a667 3 | 4 | (make-release "iao" "~/repos/information-artifact-ontology/src/ontology/iao.owl" 5 | :when 3699360000 6 | :additional-products '("ontology-metadata.owl" "iao-main")) 7 | -------------------------------------------------------------------------------- /src/ontology/ontoFox/RO_input.txt: -------------------------------------------------------------------------------- 1 | [URI of the OWL(RDF/XML) output file] 2 | http://purl.obolibrary.org/obo/iao/dev/import_RO.owl 3 | 4 | [Source ontology] 5 | RO 6 | 7 | [Low level source term URIs] 8 | http://purl.obolibrary.org/obo/RO_0001900 #temporal interpretation 9 | 10 | [Top level source term URIs and target direct superclass URIs] 11 | 12 | [Source term retrieval setting] 13 | includeNoIntermediates 14 | 15 | [Source annotation URIs] 16 | http://www.w3.org/2000/01/rdf-schema#label 17 | http://purl.obolibrary.org/obo/IAO_0000115 18 | 19 | 20 | -------------------------------------------------------------------------------- /src/tools/clean-ontofox-results.pl: -------------------------------------------------------------------------------- 1 | # Copy until the first xml comment, which leads into the annotation property section 2 | while (<>) 3 | { last if /[<][!]-- / ; 4 | # Add versionIRI 5 | if (m'') 6 | { s'OBO.owl"/>'OBO.owl">'; 7 | print $_; 8 | print ' '."\n"; 9 | print ' '."\n"; 10 | } 11 | else { 12 | print $_} 13 | } 14 | # Skip over that section 15 | while (<>) {last if /[<][!]-- /;} 16 | print " 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. 35 | temporal interpretation 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | -------------------------------------------------------------------------------- /releases/2009-11-02/merged/iao.owl: -------------------------------------------------------------------------------- 1 | 2 | 9 | 10 | 11 | 12 | 13 | $Revision$ 14 | An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at http://code.google.com/p/information-artifact-ontology/ 16 | 17 | 18 | 19 | 20 | 21 | en 22 | 23 | 24 | 25 | -------------------------------------------------------------------------------- /releases/2012-01-05/merged/iao.owl: -------------------------------------------------------------------------------- 1 | 2 | 9 | 10 | 11 | 12 | 13 | $Revision$ 14 | An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at http://code.google.com/p/information-artifact-ontology/ 16 | 17 | 18 | 19 | 20 | 21 | en 22 | 23 | 24 | 25 | -------------------------------------------------------------------------------- /releases/2017-03-24/release-notes.txt: -------------------------------------------------------------------------------- 1 | This release fixes a bug in computing inferred axioms that led to the 2 | version of 2017-03-24 getting errors when a reasoner was run on it. 3 | Use of the release of 2017-01-06 is deprecated, as one can't successfully run reasoners with it. 4 | 5 | Released versions: 6 | 7 | http://purl.obolibrary.org/obo/iao.owl 8 | http://purl.obolibrary.org/obo/iao/2017-03-24/iao.owl 9 | 10 | Retrieves a version that has all imports merged and to which inferred axioms have been added. 11 | 12 | http://purl.obolibrary.org/obo/iao/ontology-metadata.owl 13 | http://purl.obolibrary.org/obo/iao/2017-03-24/ontology-metadata.owl 14 | 15 | A version as stated (has no dependents, primarily annotation properties) 16 | 17 | http://purl.obolibrary.org/obo/iao/iao-stated.owl 18 | http://purl.obolibrary.org/obo/iao/2017-03-24/iao-stated.owl 19 | 20 | A version without inferences with import as separate files 21 | 22 | http://purl.obolibrary.org/obo/iao/iao-main.owl 23 | http://purl.obolibrary.org/obo/iao/2017-03-24/iao-main.owl 24 | 25 | As iao-stated.owl but without obsolete terms 26 | 27 | http://purl.obolibrary.org/obo/iao/dev/iao.owl 28 | http://purl.obolibrary.org/obo/iao/dev/ontology-metadata.owl 29 | http://purl.obolibrary.org/obo/iao/dev/iao-main.owl 30 | 31 | Live, direct from the repo. Can change without notice. It's probably not what you want. 32 | 33 | Main visible changes in this version: 34 | - Fix for issue #195: Reasoning error with HermiT 35 | - Partial fix for Issue #194: InverseOf axioms are stated in a verbose fashion 36 | 37 | Under the hood: 38 | - Imports refreshed 2017-03-24 39 | - BFO version http://purl.obolibrary.org/obo/bfo/2.0/bfo.owl 40 | - Stopped using inference generators InferredObjectPropertyCharacteristicAxiomGenerator and InferredSubObjectPropertyAxiomGenerator 41 | -------------------------------------------------------------------------------- /releases/2010-09-14/iao.owl: -------------------------------------------------------------------------------- 1 | 2 | 9 | 10 | 11 | 12 | 13 | 2010-09-14 14 | 15 | This file is based on checkout of our SVN repository revision $Revision: 2489 $ 16 | An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at http://code.google.com/p/information-artifact-ontology/ 18 | 19 | 20 | 21 | 22 | 23 | en 24 | 25 | 26 | 27 | -------------------------------------------------------------------------------- /releases/2009-11-06/merged/iao.owl: -------------------------------------------------------------------------------- 1 | 2 | 9 | 10 | 11 | 12 | 13 | 2009-11-06 14 | 15 | This file is based on checkout of our SVN repository revision $Revision: 2489 $ 16 | An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at http://code.google.com/p/information-artifact-ontology/ 18 | 19 | 20 | 21 | 22 | 23 | en 24 | 25 | 26 | 27 | -------------------------------------------------------------------------------- /releases/2009-11-02/ontology/IAO.owl: -------------------------------------------------------------------------------- 1 | 2 | 9 | 10 | 11 | 12 | 13 | $Revision$ 14 | An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at http://code.google.com/p/information-artifact-ontology/ 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | en 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /releases/2009-11-06/ontology/IAO.owl: -------------------------------------------------------------------------------- 1 | 2 | 9 | 10 | 11 | 12 | 13 | $Revision$ 14 | An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at http://code.google.com/p/information-artifact-ontology/ 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | en 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /releases/2012-01-05/ontology/IAO.owl: -------------------------------------------------------------------------------- 1 | 2 | 9 | 10 | 11 | 12 | 13 | $Revision$ 14 | An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at http://code.google.com/p/information-artifact-ontology/ 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | en 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /releases/2011-08-04/ontology/IAO.owl: -------------------------------------------------------------------------------- 1 | 2 | 9 | 10 | 11 | 12 | 13 | $Revision$ 14 | An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at http://code.google.com/p/information-artifact-ontology/ 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | en 26 | 27 | 28 | 29 | -------------------------------------------------------------------------------- /releases/2010-10-26/iao.owl: -------------------------------------------------------------------------------- 1 | 2 | 9 | 10 | 11 | 12 | 13 | $Revision$ 14 | An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at http://code.google.com/p/information-artifact-ontology/ 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | en 26 | 27 | 28 | 29 | -------------------------------------------------------------------------------- /releases/2012-01-05/doc/replaceIRIs.pl: -------------------------------------------------------------------------------- 1 | # The script used to replace the IRIs of BFO 1.1/RO terms with those in BFO 2.0. Since the replacement using the pattern, 2 | # be careful for the terms which shared the same pattern, such as 3 | # http://www.obofoundry.org/ro/ro.owl#has_participant 4 | # http://www.obofoundry.org/ro/ro.owl#has_part 5 | # Need to replace "has_participant" first, otherwise will cause problem 6 | 7 | # Run command under current folder: 8 | # perl replaceIRIs.pl --inFile1 termsMapping.txt -inFile2 iao-main.owl --outFile iao-main-new.owl 9 | # perl replaceIRIs.pl --inFile1 termsMapping.txt -inFile2 external.owl --outFile external-new.owl 10 | # perl replaceIRIs.pl --inFile1 termsMapping.txt -inFile2 externalByHand.owl --outFile externalByHand-new.owl 11 | # perl replaceIRIs.pl --inFile1 termsMapping.txt -inFile2 externalDerived.owl --outFile externalDerived-new.owl 12 | # perl replaceIRIs.pl --inFile1 termsMapping.txt -inFile2 ontology-metadata.owl --outFile ontology-metadata-new.owl 13 | 14 | 15 | use strict; 16 | use Getopt::Long; 17 | use IO::File; 18 | use Data::Dumper; 19 | 20 | my ($inFile1, $inFile2, $outFile); 21 | 22 | &GetOptions('inFile1=s' => \$inFile1, 23 | 'inFile2=s' => \$inFile2, 24 | 'outFile=s' => \$outFile 25 | ); 26 | 27 | my %idMaps = (); # (old IRI is the key, and new IRI is the replaced one) 28 | 29 | my $fh = IO::File->new("<$inFile1") || die "Cannot read input text file '$inFile1': $!"; 30 | 31 | while(my $line = <$fh>) { 32 | my @terms = split(/\s+/, $line); 33 | $idMaps{$terms[0]} = $terms[1]; 34 | } 35 | 36 | $fh->close(); 37 | 38 | #print Dumper(\%idMaps); 39 | #STDERR->print("size ".keys(%idMaps)."\n"); 40 | 41 | $fh = IO::File->new("<$inFile2") || die "Cannot read input text file '$inFile2': $!"; 42 | 43 | my $lineNum = 0; 44 | my $file = ""; 45 | while(my $line = <$fh>) { 46 | $file .= $line; 47 | } 48 | $fh->close(); 49 | 50 | while (my($old_iri, $new_iri) = each(%idMaps)){ 51 | $file =~ s/$old_iri/$new_iri/g; 52 | } 53 | 54 | $fh = IO::File->new(">$outFile") || die "Cannot write file '$outFile': $!"; 55 | $fh->print($file); 56 | $fh->close(); 57 | -------------------------------------------------------------------------------- /releases/2017-01-06/catalog-v001.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | -------------------------------------------------------------------------------- /releases/2017-03-24/catalog-v001.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | -------------------------------------------------------------------------------- /releases/2017-01-06/release-notes.txt: -------------------------------------------------------------------------------- 1 | This release is primarily for maintenance and requested terms 2 | 3 | Released versions: 4 | 5 | http://purl.obolibrary.org/obo/iao.owl 6 | http://purl.obolibrary.org/obo/iao/2017-01-06/iao.owl 7 | 8 | Retrieves a version that has all imports merged and to which inferred axioms have been added. 9 | 10 | http://purl.obolibrary.org/obo/iao/ontology-metadata.owl 11 | http://purl.obolibrary.org/obo/iao/2017-01-06/ontology-metadata.owl 12 | 13 | A version as stated (has no dependents, primarily annotation properties) 14 | 15 | http://purl.obolibrary.org/obo/iao/iao-stated.owl 16 | http://purl.obolibrary.org/obo/iao/2017-01-06/iao-stated.owl 17 | 18 | A version without inferences with import as separate files 19 | 20 | http://purl.obolibrary.org/obo/iao/iao-main.owl 21 | http://purl.obolibrary.org/obo/iao/2017-01-06/iao-main.owl 22 | 23 | As iao-stated.owl but without obsolete terms 24 | 25 | http://purl.obolibrary.org/obo/iao/dev/iao.owl 26 | http://purl.obolibrary.org/obo/iao/dev/ontology-metadata.owl 27 | http://purl.obolibrary.org/obo/iao/dev/iao-main.owl 28 | 29 | Live, direct from the repo. Can change without notice. It's probably not what you want. 30 | 31 | Main visible changes in this version: 32 | - Issue #187: ETL class 33 | - Issue #183: proposed extensions to IAO:'document part' and IAO:'textual entity 34 | 35 | Under the hood: 36 | - Imports refreshed 2017-01-06 37 | - A new release process reduces work required to push out new releases 38 | -- All dependents now versioned, so http://purl.obolibrary.org/iao/2017-01-06/iao-stated.owl should always load the same files 39 | -- This entailed making copies of ro/core.owl and its imports ro/bfo-axioms.owl and ro/anotations.owl which did not have versioned PURLs 40 | -- Now: http://purl.obolibrary.org/obo/iao/2017-01-06/ro/core.owl, etc. 41 | -- Copies were downloaded 2017-01-06 42 | - BFO version http://purl.obolibrary.org/obo/bfo/2.0/bfo.owl 43 | - Stopped using protege-dc instead adding declarations for those properties to ontology-metadata.owl 44 | - files no longer used deleted from repo 45 | - Consistent use of versionIRI for our files - /dev/ is versionIRI, not ontologyIRI 46 | - purl.obolibrary.org config cleaned up 47 | -------------------------------------------------------------------------------- /releases/2012-01-05/ontology_BFO2/IAO.owl: -------------------------------------------------------------------------------- 1 | 2 | 9 | 10 | An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at http://code.google.com/p/information-artifact-ontology/ 11 | en 12 | $Revision$ 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | -------------------------------------------------------------------------------- /releases/2011-05-09/iao.owl: -------------------------------------------------------------------------------- 1 | 2 | 9 | 10 | 11 | 12 | 13 | 2011-05-09 14 | 15 | An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at http://code.google.com/p/information-artifact-ontology/ 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | en 27 | 28 | 29 | 30 | -------------------------------------------------------------------------------- /docs/QC-report.csv: -------------------------------------------------------------------------------- 1 | Level,Rule Name,Subject,Property,Value,JZ comments 2 | WARN,duplicate_exact_synonym,IAO:0000609,IAO:0000118,summary@en,https://github.com/information-artifact-ontology/IAO/issues/227 3 | WARN,duplicate_exact_synonym,IAO:0000615,IAO:0000118,summary@en, 4 | WARN,missing_definition,IAO:0000004,IAO:0000115,,https://github.com/information-artifact-ontology/IAO/issues/228 5 | WARN,missing_definition,IAO:0000034,IAO:0000115,, 6 | WARN,missing_definition,IAO:0000039,IAO:0000115,, 7 | WARN,missing_definition,IAO:0000057,IAO:0000115,, 8 | WARN,missing_definition,IAO:0000404,IAO:0000115,, 9 | WARN,missing_definition,IAO:0000405,IAO:0000115,, 10 | WARN,missing_definition,IAO:0000406,IAO:0000115,, 11 | WARN,missing_definition,IAO:0000407,IAO:0000115,, 12 | WARN,missing_definition,IAO:0000429,IAO:0000115,, 13 | WARN,missing_definition,IAO:0000582,IAO:0000115,, 14 | WARN,missing_definition,http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040,IAO:0000115,,https://github.com/information-artifact-ontology/IAO/issues/230 15 | INFO,lowercase_definition,IAO:0000221,IAO:0000115,"m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q@en", 16 | INFO,lowercase_definition,IAO:0000235,IAO:0000115,inverse of the relation 'denotes'@en, 17 | INFO,lowercase_definition,IAO:0000413,IAO:0000115,relates a process to a time-measurement-datum that represents the duration of the process@en, 18 | INFO,lowercase_definition,IAO:0000417,IAO:0000115,inverse of the relation of is quality measurement of@en, 19 | INFO,lowercase_definition,IAO:0000419,IAO:0000115,inverse of the relation of is quality specification of@en, 20 | INFO,lowercase_definition,IAO:0000581,IAO:0000115,relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken@en, 21 | INFO,lowercase_definition,IAO:0000583,IAO:0000115,relates a time stamped measurement datum to the measurement datum that was measured@en, 22 | INFO,lowercase_definition,IAO:0000604,IAO:0000115,"relates a class of CRID to the date after which further instances should not be made, according to the central authority", 23 | INFO,missing_superclass,IAO:0000015,rdfs:subClassOf,,defined class 24 | INFO,missing_superclass,IAO:0000178,rdfs:subClassOf,,defined class 25 | INFO,missing_superclass,IAO:0000186,rdfs:subClassOf,,defined class -------------------------------------------------------------------------------- /releases/2012-01-05/merged/iao-inferredSuperClasses.owl: -------------------------------------------------------------------------------- 1 | 2 | 9 | 10 | 11 | 12 | 13 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | -------------------------------------------------------------------------------- /src/ontology/ontoFox/OBI_input.txt: -------------------------------------------------------------------------------- 1 | [URI of the OWL(RDF/XML) output file] 2 | http://purl.obolibrary.org/obo/iao/dev/import_OBI.owl 3 | 4 | # Retrive OBI classes 5 | [Source ontology] 6 | OBI 7 | 8 | [Low level source term URIs] 9 | http://purl.obolibrary.org/obo/OBI_0000011 #planned process 10 | http://purl.obolibrary.org/obo/OBI_0000066 #investigation 11 | http://purl.obolibrary.org/obo/OBI_0000471 #study design execution 12 | http://purl.obolibrary.org/obo/OBI_0500000 #study design 13 | http://purl.obolibrary.org/obo/OBI_0200000 #data transformation 14 | 15 | [Top level source term URIs and target direct superclass URIs] 16 | http://purl.obolibrary.org/obo/OBI_0000011 #planned process 17 | subClassOf http://purl.obolibrary.org/obo/BFO_0000015 #process 18 | http://purl.obolibrary.org/obo/OBI_0000066 #investigation 19 | subClassOf http://purl.obolibrary.org/obo/OBI_0000011 20 | http://purl.obolibrary.org/obo/OBI_0000471 #study design execution 21 | subClassOf http://purl.obolibrary.org/obo/OBI_0000011 22 | http://purl.obolibrary.org/obo/OBI_0500000 #study design 23 | subClassOf http://purl.obolibrary.org/obo/IAO_0000104 24 | http://purl.obolibrary.org/obo/OBI_0200000 #data transformation 25 | subClassOf http://purl.obolibrary.org/obo/OBI_0000011 #planned process 26 | 27 | [Source term retrieval setting] 28 | includeNoIntermediates 29 | 30 | [Source annotation URIs] 31 | http://www.w3.org/2000/01/rdf-schema#label 32 | copyTo http://purl.obolibrary.org/obo/IAO_0000111 33 | http://purl.obolibrary.org/obo/IAO_0000115 34 | 35 | 36 | ################################################### 37 | # Retrive OBI classes objectProperties 38 | [Source ontology] 39 | OBI 40 | 41 | [Low level source term URIs] 42 | http://purl.obolibrary.org/obo/OBI_0000293 #has_specified_input 43 | http://purl.obolibrary.org/obo/OBI_0000299 #has_specified_output 44 | http://purl.obolibrary.org/obo/OBI_0000312 #is_specified_output_of 45 | 46 | [Top level source term URIs and target direct superclass URIs] 47 | http://purl.obolibrary.org/obo/OBI_0000293 #has_specified_input 48 | subPropertyOf http://purl.obolibrary.org/obo/RO_0000057 #has participant 49 | http://purl.obolibrary.org/obo/OBI_0000299 #has_specified_output 50 | subPropertyOf http://purl.obolibrary.org/obo/RO_0000057 #has participant 51 | http://purl.obolibrary.org/obo/OBI_0000312 #is_specified_output_of 52 | subPropertyOf http://purl.obolibrary.org/obo/RO_0000056 #participates in 53 | 54 | [Source term retrieval setting] 55 | 56 | 57 | [Source annotation URIs] 58 | includeAllAxioms 59 | -------------------------------------------------------------------------------- /src/ontology/template/IAO_synonyms.tsv: -------------------------------------------------------------------------------- 1 | ontology ID alternative term editor note term tracker item 2 | ID AL alternative term@en SPLIT=| AL editor note@en SPLIT=| AI term tracker item 3 | IAO:0000606 abbreviation and acronyms|abbreviations and acronyms|abbreviation list|definitions for abbreviations|non-standard abbreviations|nonstandard abbreviations|nonstandard abbreviations and acronyms https://github.com/information-artifact-ontology/IAO/issues/234 4 | IAO:0000315 precis https://github.com/information-artifact-ontology/IAO/issues/234 5 | IAO:0000324 acknowledgement|acknowledgment https://github.com/information-artifact-ontology/IAO/issues/234 6 | IAO:0000323 authors' contribution|authors' contributions|authors' roles|contributorship https://github.com/information-artifact-ontology/IAO/issues/234 7 | IAO:0000607 biographies|contributor information https://github.com/information-artifact-ontology/IAO/issues/234 8 | IAO:0000611 availability of data|data archiving|data availability|data availability statement|data sharing statement https://github.com/information-artifact-ontology/IAO/issues/234 9 | IAO:0000616 conflict of interests|conflicts of interest|declaration of competing interest|declaration of interest|declaration of interests|disclosure of conflict of interest|duality of interest|statement of interest|authors' disclosures of potential conflicts of interest|competing financial interests https://github.com/information-artifact-ontology/IAO/issues/234 10 | IAO:0000319 discussions https://github.com/information-artifact-ontology/IAO/issues/234 11 | IAO:0000620 ethical requirements|ethics|ethics statement https://github.com/information-artifact-ontology/IAO/issues/234 12 | IAO:0000325 footnotes https://github.com/information-artifact-ontology/IAO/issues/234 13 | IAO:0000623 financial support|grants|role of the funding source|study funding https://github.com/information-artifact-ontology/IAO/issues/234 14 | IAO:0000625 outlook https://github.com/information-artifact-ontology/IAO/issues/234 15 | IAO:0000316 overview https://github.com/information-artifact-ontology/IAO/issues/234 16 | IAO:0000317 method|experimental methods|methodology https://github.com/information-artifact-ontology/IAO/issues/234 17 | IAO:0000320 literature cited|reference|references|reference list https://github.com/information-artifact-ontology/IAO/issues/234 18 | IAO:0000326 additional file|additional files|electronic supplementary material|electronic supplementary materials|supplemental data|supplemental material|supplementary data|supplementary files|supplementary information|supplementary materials https://github.com/information-artifact-ontology/IAO/issues/234 -------------------------------------------------------------------------------- /releases/2015-02-23/merged/iao_inferredSuperClasses.owl: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 10 | 11 | 12 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | -------------------------------------------------------------------------------- /docs/BFO 1.1 to 2.0 conversion/mapping.txt: -------------------------------------------------------------------------------- 1 | http://www.ifomis.org/bfo/1.1#Entity http://purl.obolibrary.org/obo/BFO_0000001 2 | http://www.ifomis.org/bfo/1.1/snap#Continuant http://purl.obolibrary.org/obo/BFO_0000002 3 | http://www.ifomis.org/bfo/1.1/snap#Disposition http://purl.obolibrary.org/obo/BFO_0000016 4 | http://www.ifomis.org/bfo/1.1/snap#Function http://purl.obolibrary.org/obo/BFO_0000034 5 | http://www.ifomis.org/bfo/1.1/snap#GenericallyDependentContinuant http://purl.obolibrary.org/obo/BFO_0000031 6 | http://www.ifomis.org/bfo/1.1/snap#IndependentContinuant http://purl.obolibrary.org/obo/BFO_0000004 7 | http://www.ifomis.org/bfo/1.1/snap#MaterialEntity http://purl.obolibrary.org/obo/BFO_0000040 8 | http://www.ifomis.org/bfo/1.1/snap#Quality http://purl.obolibrary.org/obo/BFO_0000019 9 | http://www.ifomis.org/bfo/1.1/snap#RealizableEntity http://purl.obolibrary.org/obo/BFO_0000017 10 | http://www.ifomis.org/bfo/1.1/snap#Role http://purl.obolibrary.org/obo/BFO_0000023 11 | http://www.ifomis.org/bfo/1.1/snap#Site http://purl.obolibrary.org/obo/BFO_0000029 12 | http://www.ifomis.org/bfo/1.1/snap#SpecificallyDependentContinuant http://purl.obolibrary.org/obo/BFO_0000020 13 | http://www.ifomis.org/bfo/1.1/span#Occurrent http://purl.obolibrary.org/obo/BFO_0000003 14 | http://www.ifomis.org/bfo/1.1/span#ProcessualEntity http://purl.obolibrary.org/obo/BFO_0000015 15 | http://www.ifomis.org/bfo/1.1/span#Process http://purl.obolibrary.org/obo/BFO_0000015 16 | http://www.ifomis.org/bfo/1.1/snap#ZeroDimensionalRegion http://purl.obolibrary.org/obo/BFO_0000018 17 | http://www.ifomis.org/bfo/1.1/snap#OneDimensionalRegion http://purl.obolibrary.org/obo/BFO_0000026 18 | http://www.ifomis.org/bfo/1.1/snap#TwoDimensionalRegion http://purl.obolibrary.org/obo/BFO_0000009 19 | http://www.ifomis.org/bfo/1.1/snap#ThreeDimensionalRegion http://purl.obolibrary.org/obo/BFO_0000028 20 | http://purl.org/obo/owl/OBO_REL#bearer_of http://purl.obolibrary.org/obo/RO_0000053 21 | http://purl.org/obo/owl/OBO_REL#inheres_in http://purl.obolibrary.org/obo/RO_0000052 22 | http://www.obofoundry.org/ro/ro.owl#has_part http://purl.obolibrary.org/obo/BFO_0000051 23 | http://www.obofoundry.org/ro/ro.owl#part_of http://purl.obolibrary.org/obo/BFO_0000050 24 | http://www.obofoundry.org/ro/ro.owl#has_participant http://purl.obolibrary.org/obo/RO_0000057 25 | http://www.obofoundry.org/ro/ro.owl#participates_in http://purl.obolibrary.org/obo/RO_0000056 26 | http://purl.obolibrary.org/obo/OBI_0000294 http://purl.obolibrary.org/obo/RO_0000059 27 | http://purl.obolibrary.org/obo/OBI_0000297 http://purl.obolibrary.org/obo/RO_0000058 28 | http://purl.obolibrary.org/obo/OBI_0000300 http://purl.obolibrary.org/obo/BFO_0000054 29 | http://purl.obolibrary.org/obo/OBI_0000308 http://purl.obolibrary.org/obo/BFO_0000055 30 | 31 | 32 | -------------------------------------------------------------------------------- /releases/2015-02-23/ontology/externalByHand.owl: -------------------------------------------------------------------------------- 1 | 2 | 13 | 14 | 15 | 16 | 23 | 24 | 25 | 26 | 27 | 34 | 35 | 36 | 37 | 38 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | -------------------------------------------------------------------------------- /src/ontology/imports/externalByHand.owl: -------------------------------------------------------------------------------- 1 | 2 | 13 | 14 | 15 | 16 | 17 | 18 | 25 | 26 | 27 | 28 | 29 | 36 | 37 | 38 | 39 | 40 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | -------------------------------------------------------------------------------- /releases/2012-07-11-BFO2/IAO.owl: -------------------------------------------------------------------------------- 1 | 2 | 11 | 12 | 13 | 14 | 15 | $Revision$ 16 | An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at http://code.google.com/p/information-artifact-ontology/ 18 | IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | en 29 | IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999 31 | 32 | 33 | IAO_0020000-IAO_0020999 34 | 35 | 36 | IAO_0021000-IAO_0021999 37 | 38 | 39 | 40 | 41 | -------------------------------------------------------------------------------- /releases/2012-01-05/doc/termsMapping.txt: -------------------------------------------------------------------------------- 1 | http://purl.org/obo/owl/OBO_REL#bearer_of http://purl.obolibrary.org/obo/BFO_0000053 2 | http://purl.org/obo/owl/OBO_REL#function_of http://purl.obolibrary.org/obo/BFO_0000079 3 | http://purl.org/obo/owl/OBO_REL#inheres_in http://purl.obolibrary.org/obo/BFO_0000052 4 | http://purl.org/obo/owl/OBO_REL#quality_of http://purl.obolibrary.org/obo/BFO_0000080 5 | http://purl.org/obo/owl/OBO_REL#role_of http://purl.obolibrary.org/obo/BFO_0000081 6 | http://www.ifomis.org/bfo/1.1#Entity http://purl.obolibrary.org/obo/BFO_0000001 7 | http://www.ifomis.org/bfo/1.1/snap#Continuant http://purl.obolibrary.org/obo/BFO_0000002 8 | http://www.ifomis.org/bfo/1.1/snap#DependentContinuant http://purl.obolibrary.org/obo/BFO_0000005 9 | http://www.ifomis.org/bfo/1.1/snap#Disposition http://purl.obolibrary.org/obo/BFO_0000016 10 | http://www.ifomis.org/bfo/1.1/snap#Function http://purl.obolibrary.org/obo/BFO_0000034 11 | http://www.ifomis.org/bfo/1.1/snap#GenericallyDependentContinuant http://purl.obolibrary.org/obo/BFO_0000031 12 | http://www.ifomis.org/bfo/1.1/snap#IndependentContinuant http://purl.obolibrary.org/obo/BFO_0000004 13 | http://www.ifomis.org/bfo/1.1/snap#MaterialEntity http://purl.obolibrary.org/obo/BFO_0000040 14 | http://www.ifomis.org/bfo/1.1/snap#Quality http://purl.obolibrary.org/obo/BFO_0000019 15 | http://www.ifomis.org/bfo/1.1/snap#RealizableEntity http://purl.obolibrary.org/obo/BFO_0000017 16 | http://www.ifomis.org/bfo/1.1/snap#Role http://purl.obolibrary.org/obo/BFO_0000023 17 | http://www.ifomis.org/bfo/1.1/snap#Site http://purl.obolibrary.org/obo/BFO_0000029 18 | http://www.ifomis.org/bfo/1.1/snap#SpecificallyDependentContinuant http://purl.obolibrary.org/obo/BFO_0000020 19 | http://www.ifomis.org/bfo/1.1/span#Occurrent http://purl.obolibrary.org/obo/BFO_0000003 20 | http://www.ifomis.org/bfo/1.1/span#Process http://purl.obolibrary.org/obo/BFO_0000007 21 | http://www.ifomis.org/bfo/1.1/span#ProcessualEntity http://purl.obolibrary.org/obo/BFO_0000007 22 | http://www.obofoundry.org/ro/ro.owl#has_participant http://purl.obolibrary.org/obo/BFO_0000057 23 | http://www.obofoundry.org/ro/ro.owl#has_part http://purl.obolibrary.org/obo/BFO_0000051 24 | http://www.obofoundry.org/ro/ro.owl#located_in http://purl.obolibrary.org/obo/BFO_0000082 25 | http://www.obofoundry.org/ro/ro.owl#part_of http://purl.obolibrary.org/obo/BFO_0000050 26 | http://www.obofoundry.org/ro/ro.owl#participates_in http://purl.obolibrary.org/obo/BFO_0000056 27 | http://www.obofoundry.org/ro/ro.owl#preceded_by http://purl.obolibrary.org/obo/BFO_0000060 28 | http://www.ifomis.org/bfo/1.1/snap#ZeroDimensionalRegion http://purl.obolibrary.org/obo/BFO_0000018 29 | http://www.ifomis.org/bfo/1.1/snap#OneDimensionalRegion http://purl.obolibrary.org/obo/BFO_0000026 30 | http://www.ifomis.org/bfo/1.1/snap#TwoDimensionalRegion http://purl.obolibrary.org/obo/BFO_0000009 31 | http://www.ifomis.org/bfo/1.1/snap#ThreeDimensionalRegion http://purl.obolibrary.org/obo/BFO_0000028 32 | http://purl.obolibrary.org/obo/OBI_0000294 http://purl.obolibrary.org/obo/BFO_0000059 33 | http://purl.obolibrary.org/obo/OBI_0000297 http://purl.obolibrary.org/obo/BFO_0000058 34 | http://purl.obolibrary.org/obo/OBI_0000300 http://purl.obolibrary.org/obo/BFO_0000054 35 | http://purl.obolibrary.org/obo/OBI_0000308 http://purl.obolibrary.org/obo/BFO_0000055 36 | 37 | -------------------------------------------------------------------------------- /src/ontology/imports/import_UO.owl: -------------------------------------------------------------------------------- 1 | 2 | 10 | 11 | 12 | 13 | 14 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | length unit 59 | 60 | length unit 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | mass unit 70 | 71 | mass unit 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | time unit 81 | 82 | time unit 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | -------------------------------------------------------------------------------- /src/ontology/template/IAO_newTerms.tsv: -------------------------------------------------------------------------------- 1 | Ontology ID Label editor preferred term has curation status alternative term definition definition source example of usage editor note term editor curator note ontology term requester term tracker item Parent Logic Axioms 2 | ID AL rdfs:label@en AL editor preferred term@en AI has curation status AL alternative term@en SPLIT=| AL definition@en A definition source SPLIT=| AL example of usage@en SPLIT=| AL editor note@en SPLIT=| A term editor SPLIT=| AL curator note@en SPLIT=| A ontology term requester AI term tracker item C % SPLIT=| C % SPLIT=| 3 | IAO:0000701 descriptive data section descriptive data section metadata complete "A document part that lists and defines data variables, describes data characteristics (e.g. missing data information) and any assumptions and simplifications made." https://www.equator-network.org/reporting-guidelines/prisma/ PERSON: Chen Yang|PERSON: Jie Zheng ONE ontology https://github.com/information-artifact-ontology/IAO/issues/235 document part 4 | IAO:0000702 additional results section additional results section metadata complete "A results section that reports analyses other than main results of the study (e.g. subgroups analyses, adjusted analyses, sensitivity analyses, etc.)" https://www.equator-network.org/reporting-guidelines/strobe/|https://www.equator-network.org/reporting-guidelines/consort/|https://www.equator-network.org/reporting-guidelines/prisma/ PERSON: Chen Yang|PERSON: Jie Zheng ONE ontology https://github.com/information-artifact-ontology/IAO/issues/235 results section 5 | IAO:0000703 research participants section research participants section metadata complete "A document part that describes human subject(s) that participated in a study (e.g. inclusion & exclusion criteria, recruitment methods, reasons for non-participation, grouping and randomisation, methods of follow-up, etc.)." https://www.equator-network.org/reporting-guidelines/consort/|https://www.equator-network.org/reporting-guidelines/strobe-nut/|https://www.equator-network.org/reporting-guidelines/prisma/ PERSON: Chen Yang|PERSON: Jie Zheng ONE ontology https://github.com/information-artifact-ontology/IAO/issues/235 document part 6 | IAO:0000704 measurement methods section measurement methods section metadata complete A methods section that describes details of data assessment methods (data measurement). https://www.equator-network.org/reporting-guidelines/strobe/ PERSON: Chen Yang|PERSON: Jie Zheng ONE ontology https://github.com/information-artifact-ontology/IAO/issues/235 methods section 7 | IAO:0000705 research settings section research settings section metadata complete A document part that describes the physical/social/cultural conditions around a research trial. https://www.ncbi.nlm.nih.gov/books/NBK262175/ PERSON: Chen Yang|PERSON: Jie Zheng ONE ontology https://github.com/information-artifact-ontology/IAO/issues/235 document part 8 | IAO:0000706 study bias section study bias section metadata complete A study limitations section that describes systematic error introduced into sampling or testing by selecting or encouraging one outcome or answer over others. DOI: 10.1097/PRS.0b013e3181de24bc PERSON: Chen Yang|PERSON: Jie Zheng ONE ontology https://github.com/information-artifact-ontology/IAO/issues/235 study limitations section 9 | IAO:0000707 graphical abstract graphical abstract metadata complete visual abstract An abstract that is pictorial summary of the main findings described in the document. https://www.elsevier.com/authors/journal-authors/graphical-abstract PERSON: Tim Beck|PERSON: Jie Zheng Biomedical literature NLP project https://github.com/information-artifact-ontology/IAO/issues/234 abstract -------------------------------------------------------------------------------- /releases/2017-01-06/ro/bfo-axioms.owl: -------------------------------------------------------------------------------- 1 | 2 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | -------------------------------------------------------------------------------- /releases/2017-03-24/ro/bfo-axioms.owl: -------------------------------------------------------------------------------- 1 | 2 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- 1 | # config 2 | MAKEFLAGS += --warn-undefined-variables 3 | SHELL := bash 4 | .SHELLFLAGS := -eu -o pipefail -c 5 | .DEFAULT_GOAL := all 6 | .DELETE_ON_ERROR: 7 | .SUFFIXES: 8 | 9 | # Run `make all` to create a new IAO release: 10 | # - download the latest build of ROBOT 11 | # - merge iao-edit.owl with imports to create iao-merged.owl 12 | # - reason over iao-merged.owl to create iao.owl 13 | # - clean build files 14 | 15 | # If you wish to keep build/robot.jar, run `make release` instead. 16 | 17 | # =============================== 18 | # VARIABLES 19 | # =============================== 20 | 21 | SHELL := /bin/bash 22 | OBO := http://purl.obolibrary.org/obo 23 | DEV := $(OBO)/iao/dev 24 | ROBOT := java -jar build/robot.jar 25 | 26 | # release vars 27 | TODAY := $(shell date +%Y-%m-%d) 28 | TS := $(shell date +'%d:%m:%Y %H:%M') 29 | 30 | # directories 31 | SRC = src/ontology 32 | 33 | 34 | # =============================== 35 | # MAIN TASK 36 | # =============================== 37 | 38 | # run `make all` or `make release` to make a new release 39 | # `make all` will remove the build dir with ROBOT on completion 40 | all: clean 41 | 42 | ### Directories 43 | # 44 | # This is a temporary place to put things. 45 | build: 46 | mkdir -p $@ 47 | 48 | # =============================== 49 | # ROBOT 50 | # =============================== 51 | 52 | # download the most recent build of ROBOT 53 | build/robot.jar: | build 54 | @echo "Getting ROBOT" && \ 55 | curl -L -o $@ https://github.com/ontodev/robot/releases/download/v1.6.0/robot.jar 56 | 57 | 58 | clean: | release 59 | @echo "Removing build files" && \ 60 | rm -rf build 61 | 62 | # =============================== 63 | # IAO TASKS 64 | # =============================== 65 | 66 | # Update import file, commented on this release 67 | # regenerate fresh import-OBO file 68 | # .PHONY: src/ontology/import-OBO.owl 69 | # $(SRC)/import-OBO.owl: 70 | # @echo "Generating $@" && \ 71 | # cd src/ontology/ontofox && \ 72 | # curl -s -F file=@OntoFox-input.txt http://ontofox.hegroup.org/service.php > ../import-OBO.owl 73 | 74 | ### Imports 75 | # 76 | # Use Ontofox to import various modules. 77 | build/import_%.owl: src/ontology/ontoFox/%_input.txt | build/robot.jar build 78 | curl -s -F file=@$< -o $@ https://ontofox.hegroup.org/service.php 79 | 80 | # Use ROBOT to remove external java axioms 81 | src/ontology/imports/import_%.owl: build/import_%.owl 82 | $(ROBOT) remove --input build/import_$*.owl \ 83 | --base-iri 'http://purl.obolibrary.org/obo/$*_' \ 84 | --axioms external \ 85 | --preserve-structure false \ 86 | --trim false \ 87 | --output $@ 88 | 89 | IMPORT_FILES := $(wildcard src/ontology/imports/import_*.owl) 90 | 91 | .PHONY: imports 92 | imports: $(IMPORT_FILES) 93 | 94 | 95 | # merge components to generate iao-merged 96 | build/iao-merged.owl: $(SRC)/iao-edit.owl | build/robot.jar build 97 | @echo "Merging $< to $@" && \ 98 | $(ROBOT) merge \ 99 | --input $< \ 100 | annotate \ 101 | --ontology-iri "$(OBO)/iao/iao-merged.owl" \ 102 | --version-iri "$(OBO)/iao/$(TODAY)/iao-merged.owl" \ 103 | --annotation owl:versionInfo "$(TODAY)" \ 104 | --output build/iao_merged.tmp.owl 105 | sed '/ $@ 106 | rm build/iao_merged.tmp.owl 107 | 108 | # reason over iao-merged to generate IAO 109 | iao.owl: build/iao-merged.owl 110 | @echo "Reasoning $< to $@" && \ 111 | $(ROBOT) reason \ 112 | --input $< \ 113 | --reasoner HermiT \ 114 | --exclude-tautologies all \ 115 | annotate \ 116 | --ontology-iri "$(OBO)/iao.owl" \ 117 | --version-iri "$(OBO)/iao/$(TODAY)/iao.owl" \ 118 | --annotation owl:versionInfo "$(TODAY)" \ 119 | --output $@ 120 | 121 | ### Test 122 | # 123 | # Run tests 124 | 125 | # Run a reasoner to find inconsistencies 126 | .PHONY: reason 127 | reason: build/iao-merged.owl | build/robot.jar 128 | @echo "Running tests" 129 | @echo "Run reasoning" 130 | $(ROBOT) reason --input $< --reasoner hermit --equivalent-classes-allowed none 131 | 132 | # Run robot report 133 | build/robot-report.tsv: build/iao-merged.owl 134 | @echo "Generate robot report ignoring term IAO_0000118 alternative label" 135 | $(ROBOT) remove \ 136 | --input $< \ 137 | --term IAO:0000118 \ 138 | report \ 139 | --fail-on error \ 140 | --output $@ 141 | 142 | .PHONY: test 143 | test: reason build/robot-report.tsv 144 | 145 | release: build/iao-merged.owl iao.owl 146 | @echo "A new release is made" 147 | 148 | 149 | -------------------------------------------------------------------------------- /releases/2010-09-14/external/protege.owl: -------------------------------------------------------------------------------- 1 | 2 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | -------------------------------------------------------------------------------- /releases/2011-05-09/external/protege.owl: -------------------------------------------------------------------------------- 1 | 2 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | -------------------------------------------------------------------------------- /releases/2012-01-05/ontology_BFO2/external.owl: -------------------------------------------------------------------------------- 1 | 2 | 16 | 17 | $Revision: 80 $ 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | has curation status 63 | 64 | 65 | term editor 66 | 67 | 68 | definition source 69 | 70 | 71 | imported from 72 | 73 | 74 | example of usage 75 | 76 | 77 | definition 78 | 79 | 80 | alternative term 81 | 82 | 83 | editor preferred term 84 | 85 | 86 | editor note 87 | 88 | 89 | in branch 90 | 91 | 92 | 93 | 94 | -------------------------------------------------------------------------------- /releases/2017-01-06/externalByHand.owl: -------------------------------------------------------------------------------- 1 | 2 | 11 | 12 | 13 | http://creativecommons.org/licenses/by/4.0/ 14 | The Information Artifact Ontology (IAO) is licensed under the Creative Commons Attribution License (CC-BY) version 4.0. You are free to share (copy and redistribute the material in any medium or format) and adapt (remix, transform, and build upon the material) for any purpose, even commercially. for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the license terms. You must give appropriate credit (by using the original ontology IRI for the whole ontology and original term IRIs for individual terms), provide a link to the license, and indicate if any changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. For more information see http://www.obofoundry.org/docs/Citation.html 15 | 16 | 17 | 18 | 19 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | geographic location 105 | A reference to a place on the Earth, by its name or by its geographical location. 106 | 107 | geographic location 108 | 109 | 110 | 111 | 112 | 113 | 114 | 115 | 116 | 117 | 118 | 119 | 120 | 121 | -------------------------------------------------------------------------------- /releases/2017-03-24/externalByHand.owl: -------------------------------------------------------------------------------- 1 | 2 | 11 | 12 | 13 | http://creativecommons.org/licenses/by/4.0/ 14 | The Information Artifact Ontology (IAO) is licensed under the Creative Commons Attribution License (CC-BY) version 4.0. You are free to share (copy and redistribute the material in any medium or format) and adapt (remix, transform, and build upon the material) for any purpose, even commercially. for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the license terms. You must give appropriate credit (by using the original ontology IRI for the whole ontology and original term IRIs for individual terms), provide a link to the license, and indicate if any changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. For more information see http://www.obofoundry.org/docs/Citation.html 15 | 16 | 17 | 18 | 19 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | geographic location 105 | A reference to a place on the Earth, by its name or by its geographical location. 106 | 107 | geographic location 108 | 109 | 110 | 111 | 112 | 113 | 114 | 115 | 116 | 117 | 118 | 119 | 120 | 121 | -------------------------------------------------------------------------------- /releases/2011-08-04/merged/iao.owl: -------------------------------------------------------------------------------- 1 | 2 | 10 | 11 | 12 | 13 | 14 | 2011-08-04 15 | 16 | This file is based on checkout of our SVN repository revision $Revision: 506 $ 17 | An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at http://code.google.com/p/information-artifact-ontology/ 19 | 20 | 21 | 22 | 23 | 24 | en 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | ICBO2011 release 38 | 39 | 40 | SVN $Revision: 506 $ 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | -------------------------------------------------------------------------------- /releases/2012-01-05/ontology/external.owl: -------------------------------------------------------------------------------- 1 | 2 | 16 | 17 | $Revision: 80 $ 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | has curation status 69 | 70 | 71 | term editor 72 | 73 | 74 | definition source 75 | 76 | 77 | imported from 78 | 79 | 80 | example of usage 81 | 82 | 83 | definition 84 | 85 | 86 | alternative term 87 | 88 | 89 | editor preferred term 90 | 91 | 92 | editor note 93 | 94 | 95 | in branch 96 | 97 | 98 | 99 | 100 | -------------------------------------------------------------------------------- /src/ontology/imports/import_PATO.owl: -------------------------------------------------------------------------------- 1 | 2 | 10 | 11 | 12 | 13 | 14 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | morphology 65 | A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. 66 | 67 | morphology 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | length 77 | A 1-D extent quality which is equal to the distance between two points. 78 | 79 | length 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | mass 89 | A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. 90 | 91 | mass 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 | physical quality 101 | A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. 102 | 103 | physical quality 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | physical object quality 113 | A quality which inheres in a continuant. 114 | 115 | physical object quality 116 | 117 | 118 | 119 | 120 | 121 | 122 | 123 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | [![Powered by the ROBOT](https://img.shields.io/static/v1?label=Powered%20by&message=ROBOT&color=green&style=flat)](http://robot.obolibrary.org/) 2 | 3 | 4 | 5 | # information artifact ontology (IAO) 6 | 7 | The Information Artifact Ontology (IAO) is a new ontology of information entities, originally driven by work by the [OBI](http://obi-ontology.org/) digital entity and realizable information entity branch. 8 | 9 | The IAO mailing-list is available at http://groups.google.com/group/information-ontology 10 | 11 | ### Files 12 | 13 | |Version|Filename|PURL Link| 14 | |---|---|---| 15 | |Release|iao.owl|http://purl.obolibrary.org/obo/iao.owl| 16 | |Development|iao-edit.owl|http://purl.obolibrary.org/obo/iao/dev/iao-edit.owl| 17 | 18 | The development version IAO (iao-edit.owl) imports all ontologies/files needed for the full version of the IAO ontology: 19 | - [Basic Formal Ontology](http://purl.obolibrary.org/obo/bfo.owl): latest release 20 | - [OBO Metadata Ontology](http://purl.obolibrary.org/obo/omo.owl): latest release 21 | - [Relation Ontology Core subset](http://purl.obolibrary.org/obo/ro/core.owl): latest release 22 | - [import-OBO.owl](http://purl.obolibrary.org/obo/iao/dev/import-OBO.owl): reused terms in external ontologies, retrieved using ontoFox tool 23 | - [externalByHand.owl](http://purl.obolibrary.org/obo/iao/dev/externalByHand.owl): terms or axioms associated with terms in external ontologies, added manually 24 | - [obsolete.owl](http://purl.obolibrary.org/obo/iao/dev/obsolete.owl): obsolete classes and properties 25 | 26 | OBO Metadata Ontology (OMO) was part of the IAO, developed in a separate OWL file. It contains [metadata properties](https://github.com/information-artifact-ontology/IAO/wiki/OntologyMetadata) that have been widely used by many OBO Foundry ontologies. In early 2020, it was registered as an indepentent ontology. Please check the OBO Metadata Ontology (OMO) on the [ontology-metadata repository](https://github.com/information-artifact-ontology/ontology-metadata). 27 | 28 | A reasonable place to start browsing the IAO is at the terms [information content entity](http://purl.obolibrary.org/obo/IAO_0000030) or [data item](http://purl.obolibrary.org/obo/IAO_0000027) or the property [is about](http://purl.obolibrary.org/obo/IAO_0000136). 29 | 30 | ### Conference calls 31 | 32 | IAO conference calls take place on an occasional basis, usually via Skype. Information about those is posted on our [mailing-list](http://groups.google.com/group/information-ontology), and agenda and minutes are available [here](https://github.com/information-artifact-ontology/IAO/wiki/Meeting_notes). 33 | Anybody is welcome to join at any time. 34 | 35 | ### Credits 36 | 37 | The IAO is a descendant of the [DENRIE branch](http://ashby.csail.mit.edu/presentations/DenrieReport.pdf) of the [OBI Project](http://obi-ontology.org/), edited by [Chris Stoeckert](http://www.cbil.upenn.edu/~stoeckrt/home.html) and other [IAO team members](https://github.com/information-artifact-ontology/IAO/wiki/AdditionalCredits). 38 | 39 | ### Presentations and Meetings 40 | 41 | The [first workshop](https://web.archive.org/web/20170712204335/http://neurocommons.org/page/First_IAO_workshop) on the IAO took place in Boston at the MIT Stata Center, June 9, 2008. 42 | 43 | In July 2009, a tutorial [From Basic Formal Ontology to the Information Artifact Ontology](http://www.bioontology.org/wiki/index.php/From_BFO_to_IAO) was presented, colocated at the [ICBO: International Conference on Biomedical Ontology](http://icbo.buffalo.edu/). Slides that include a section on topics in the IAO are [here](http://icbo.buffalo.edu/Presentations/Ruttenberg.pdf). Other [presentations may be of interest](http://icbo.buffalo.edu/Presentations/). 44 | 45 | In July 2011, a workshop was held co-located with ICBO, dealing with adverse event representation based on IAO and [OGMS](http://purl.obolibrary.org/obo/ogms). See http://purl.org/net/aeicbo2011. A [working session](https://github.com/information-artifact-ontology/IAO/wiki/WorkingSessionICBO2011) was organized on Friday July 29th 2011. 46 | 47 | In May 2012, [a meeting discussing a signature discovery ontology](http://ncorwiki.buffalo.edu/index.php/Basic_Formal_Ontology_and_the_Signature_Discovery_Ontology), much of which was concerned with future development of IAO. 48 | 49 | A [working session on IAO](https://github.com/information-artifact-ontology/IAO/wiki/WorkingSessionICBO2012) was held on Saturday July 21st, 2012, 6-8pm during the ICBO 2012 conference. 50 | 51 | ### Projects known to be using IAO 52 | 53 | - [The Ontology for Biomedical Investigations](http://ob-ontology.org) 54 | - [The Oral Health and Disease Ontology](http://code.google.com/p/ohd-ontology) 55 | - [The OWL format for OBO ontologies](http://code.google.com/p/oboformat/) 56 | - [KIAO](http://bio-ontologies.knowledgeblog.org/149) 57 | - [the Ontology for General Medical Science](https://github.com/OGMS/ogms) 58 | 59 | and as listed on IAO's [BioPortal](http://bioportal.bioontology.org/ontologies/1393) page: 60 | - [An Ontology for Drug Discovery Investigations (DDI)](http://purl.org/ddi/home) 61 | - [Adverse Event Reporting Ontology (AERO) ](http://purl.obolibrary.org/obo/aero) 62 | - [ISA software suite ](http://isa-tools.org/) 63 | - [NCBO Resource Index ](http://www.bioontology.org/resources-index) 64 | - [Ontology of Data Mining (OntoDM) ](http://kt.ijs.si/panovp/OntoDM/) 65 | - [Neural ElectroMagnetic Ontologies (NEMO) ](http://nemo.nic.uoregon.edu/) 66 | - [Influenza Research Database (IRD) ](http://bioportal.bioontology.org/ontologies/www.fludb.org) 67 | - [OntoCAT ](http://www.ontocat.org/) 68 | - [eagle-i ](https://www.eagle-i.org/home/) 69 | -------------------------------------------------------------------------------- /releases/2011-05-09/external.owl: -------------------------------------------------------------------------------- 1 | 2 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | has curation status 78 | 79 | 80 | definition editor 81 | 82 | 83 | definition source 84 | 85 | 86 | imported from 87 | 88 | 89 | example of usage 90 | 91 | 92 | definition 93 | 94 | 95 | alternative term 96 | 97 | 98 | editor preferred term 99 | 100 | 101 | editor note 102 | 103 | 104 | in branch 105 | 106 | 107 | 108 | 109 | -------------------------------------------------------------------------------- /releases/2010-10-26/external.owl: -------------------------------------------------------------------------------- 1 | 2 | 32 | 33 | $Revision: 80 $ 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | has curation status 79 | 80 | 81 | definition editor 82 | 83 | 84 | definition source 85 | 86 | 87 | imported from 88 | 89 | 90 | example of usage 91 | 92 | 93 | definition 94 | 95 | 96 | alternative term 97 | 98 | 99 | editor preferred term 100 | 101 | 102 | editor note 103 | 104 | 105 | in branch 106 | 107 | 108 | 109 | 110 | -------------------------------------------------------------------------------- /releases/2011-08-04/ontology/external.owl: -------------------------------------------------------------------------------- 1 | 2 | 32 | 33 | $Revision: 80 $ 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | has curation status 79 | 80 | 81 | term editor 82 | 83 | 84 | definition source 85 | 86 | 87 | imported from 88 | 89 | 90 | example of usage 91 | 92 | 93 | definition 94 | 95 | 96 | alternative term 97 | 98 | 99 | editor preferred term 100 | 101 | 102 | editor note 103 | 104 | 105 | in branch 106 | 107 | 108 | 109 | 110 | -------------------------------------------------------------------------------- /releases/2009-11-02/ontology/external.owl: -------------------------------------------------------------------------------- 1 | 2 | 32 | 33 | $Revision: 80 $ 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | has curation status 79 | 80 | 81 | definition editor 82 | 83 | 84 | definition source 85 | 86 | 87 | imported from 88 | 89 | 90 | example of usage 91 | 92 | 93 | definition 94 | 95 | 96 | alternative term 97 | 98 | 99 | editor preferred term 100 | 101 | 102 | editor note 103 | 104 | 105 | in branch 106 | 107 | 108 | 109 | 110 | -------------------------------------------------------------------------------- /releases/2009-11-06/ontology/external.owl: -------------------------------------------------------------------------------- 1 | 2 | 32 | 33 | $Revision: 80 $ 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | has curation status 79 | 80 | 81 | definition editor 82 | 83 | 84 | definition source 85 | 86 | 87 | imported from 88 | 89 | 90 | example of usage 91 | 92 | 93 | definition 94 | 95 | 96 | alternative term 97 | 98 | 99 | editor preferred term 100 | 101 | 102 | editor note 103 | 104 | 105 | in branch 106 | 107 | 108 | 109 | 110 | -------------------------------------------------------------------------------- /releases/2010-09-14/external.owl: -------------------------------------------------------------------------------- 1 | 2 | 32 | 33 | http://purl.obolibrary.org/obo/iao/2010-09-14/external.owl 34 | 35 | $Revision: 80 $ 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | has curation status 81 | 82 | 83 | definition editor 84 | 85 | 86 | definition source 87 | 88 | 89 | imported from 90 | 91 | 92 | example of usage 93 | 94 | 95 | definition 96 | 97 | 98 | alternative term 99 | 100 | 101 | editor preferred term 102 | 103 | 104 | editor note 105 | 106 | 107 | in branch 108 | 109 | 110 | 111 | 112 | -------------------------------------------------------------------------------- /src/example/community-label.owl: -------------------------------------------------------------------------------- 1 | 2 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | within community 33 | Person:Alan Ruttenberg 34 | relation between (an association between an alternative term and an entity) and a community in which the term is considered a preferred label for the entity 35 | 36 | 37 | 38 | 39 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | community of practice 54 | 55 | 2010/03/06 Alan Ruttenberg: Currently a placeholder. Probably to be either defined in a manner analogous to organization or population. For talking about entities like the people in a certain lab, or toxicologists, or clinicians in the united states. The immediate use is to be able to associate some synonym with a community that uses it preferentially. 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | microarray 64 | 65 | A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position. 66 | array 67 | 68 | 69 | 70 | array 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | data item 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | Material entity 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 114 | 115 | 116 | 117 | 118 | 119 | 120 | 121 | 122 | transcriptomics researcher community 123 | 124 | 125 | 126 | 127 | 128 | 129 | 130 | 131 | Ontology for Biomedical Investigations 132 | 133 | 134 | 135 | 136 | 137 | 138 | 139 | -------------------------------------------------------------------------------- /releases/2015-02-23/ontology/IAO.owl: -------------------------------------------------------------------------------- 1 | 2 | 11 | 12 | An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at http://code.google.com/p/information-artifact-ontology/ 13 | IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999 14 | IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999 15 | This is a transitional artifact for discussion, not to be used for production 16 | en 17 | $Revision$ 18 | 19 | Adam Goldstein 20 | Alan Ruttenberg 21 | Albert Goldfain 22 | Barry Smith 23 | Bjoern Peters 24 | Carlo Torniai 25 | Chris Mungall 26 | Chris Stoeckert 27 | Christian A. Boelling 28 | Darren Natale 29 | David Osumi-Sutherland 30 | Gwen Frishkoff 31 | Holger Stenzhorn 32 | James A. Overton 33 | James Malone 34 | Jennifer Fostel 35 | Jie Zheng 36 | Jonathan Rees 37 | Larisa Soldatova 38 | Lawrence Hunter 39 | Mathias Brochhausen 40 | Matt Brush 41 | Melanie Courtot 42 | Michel Dumontier 43 | Yongqun (Oliver) He 44 | Paolo Ciccarese 45 | Pat Hayes 46 | Philippe Rocca-Serra 47 | Randy Dipert 48 | Ron Rudnicki 49 | Satya Sahoo 50 | Sivaram Arabandi 51 | Werner Ceusters 52 | William Duncan 53 | William Hogan 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 90 | 91 | 92 | IAO_0020000-IAO_0020999 93 | 94 | 95 | IAO_0021000-IAO_0021999 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | -------------------------------------------------------------------------------- /src/tools/build/IAOTools/src/ca/bccrc/iao/IAOIdUpdater.java: -------------------------------------------------------------------------------- 1 | 2 | package ca.bccrc.iao; 3 | 4 | import java.net.URI; 5 | import java.net.URISyntaxException; 6 | import java.text.NumberFormat; 7 | import java.util.ArrayList; 8 | import java.util.HashSet; 9 | 10 | 11 | import org.semanticweb.owl.apibinding.OWLManager; 12 | import org.semanticweb.owl.model.AddAxiom; 13 | import org.semanticweb.owl.model.OWLAnnotation; 14 | import org.semanticweb.owl.model.OWLAxiom; 15 | import org.semanticweb.owl.model.OWLClass; 16 | import org.semanticweb.owl.model.OWLDataFactory; 17 | import org.semanticweb.owl.model.OWLEntity; 18 | import org.semanticweb.owl.model.OWLOntology; 19 | import org.semanticweb.owl.model.OWLOntologyChangeException; 20 | import org.semanticweb.owl.model.OWLOntologyCreationException; 21 | import org.semanticweb.owl.model.OWLOntologyManager; 22 | import org.semanticweb.owl.model.OWLOntologyStorageException; 23 | import org.semanticweb.owl.model.UnknownOWLOntologyException; 24 | import org.semanticweb.owl.util.OWLEntityRenamer; 25 | import org.semanticweb.owl.vocab.OWLRDFVocabulary; 26 | 27 | 28 | /** 29 | * @author mcourtot 30 | * 31 | */ 32 | public class IAOIdUpdater { 33 | 34 | 35 | // create a list to store changes in 36 | 37 | 38 | public static NumberFormat uriIDFormat = new java.text.DecimalFormat("0000000"); 39 | 40 | public static ArrayList listUsedIDs = new ArrayList(); 41 | public static ArrayList listToModifyIDs = new ArrayList(); 42 | 43 | /** 44 | * @param ontology 45 | * @return the list of IDs already in use 46 | */ 47 | public static void IDUsedChecker(OWLOntology ontology){ 48 | 49 | //this covers datatype- and object- properties, individuals and classes 50 | for(OWLEntity singleClass : ontology.getReferencedEntities()) { 51 | 52 | URI singleClassURI = singleClass.getURI(); 53 | 54 | if (singleClassURI.toString().matches("http://purl.obofoundry.org/obo/(.*)")) 55 | { 56 | 57 | //check if ID correct format 58 | if (singleClass.toString().matches("IAO_[0-9]{7}")){ 59 | listUsedIDs.add(singleClass.getURI()); 60 | } 61 | else { 62 | listToModifyIDs.add(singleClass.getURI()); 63 | } 64 | 65 | } 66 | } 67 | 68 | 69 | //of course, annotations are different.. 70 | for (URI annotationURI : ontology.getAnnotationURIs()){ 71 | listUsedIDs.add(annotationURI); 72 | } 73 | 74 | 75 | } 76 | 77 | 78 | /** 79 | * @param uriCount - the ID we want to assign 80 | * @return the next free ID 81 | * @throws URISyntaxException 82 | */ 83 | public static int getNextFreeID(int uriCount) throws URISyntaxException { 84 | 85 | 86 | String newID = uriIDFormat.format(new Integer(uriCount)); 87 | 88 | URI uriName = new URI("http://purl.obofoundry.org/obo/IAO_"+newID); 89 | 90 | if (!listUsedIDs.contains(uriName)){ 91 | //this ID is free, return it 92 | return uriCount; 93 | } 94 | 95 | else { 96 | //ID was already taken 97 | //increment counter 98 | uriCount++; 99 | //retry with this new ID 100 | return getNextFreeID(uriCount); 101 | } 102 | 103 | } 104 | 105 | 106 | 107 | /** 108 | * @param args 109 | */ 110 | public static void main(String[] args){ 111 | 112 | 113 | 114 | //Create OWLOntologyManager which manages a set of ontologies 115 | 116 | OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); 117 | 118 | 119 | // original file to load 120 | URI physicalURI = URI.create("file:/Users/mcourtot/Desktop/projects/IAO/SVN/trunk/src/ontology/IAO.owl"); 121 | // where to save the resulting file 122 | URI physicalURI2 = URI.create("file:/Users/mcourtot/Desktop/IAO_IDsOK.owl"); 123 | 124 | 125 | // Now ask the manager to load the ontology 126 | OWLOntology ontology = null; 127 | try { 128 | ontology = manager.loadOntologyFromPhysicalURI(physicalURI); 129 | } catch (OWLOntologyCreationException e) { 130 | e.printStackTrace(); 131 | } 132 | 133 | //create the converter, first of all add ontology to a set for the constructor 134 | java.util.Set ontologySet = new HashSet(); 135 | ontologySet.add(ontology); 136 | OWLEntityRenamer classRenamer = new OWLEntityRenamer(manager, ontologySet); 137 | 138 | OWLDataFactory df = manager.getOWLDataFactory(); 139 | 140 | //build the list of already used IDs, and list of IDs to modify 141 | IDUsedChecker(ontology); 142 | 143 | int uriCount = 1; 144 | //browse the ones to modify 145 | for (URI toModify : listToModifyIDs) { 146 | System.out.println("to modify: "+toModify.toString()); 147 | try { 148 | uriCount = getNextFreeID(1); 149 | } catch (URISyntaxException e) { 150 | e.printStackTrace(); 151 | } 152 | 153 | String newID = uriIDFormat.format(new Integer(uriCount)); 154 | URI uriName = null; 155 | try { 156 | uriName = new URI("http://purl.obofoundry.org/obo/IAO_"+newID); 157 | } catch (URISyntaxException e) { 158 | e.printStackTrace(); 159 | } 160 | 161 | /* keep the current ID as label if we don't already have one - eg http://purl.obofoundry.org/obo/String: we want to add String as label for the class */ 162 | OWLClass classToModify = df.getOWLClass(toModify); 163 | //check if the class we are modifying already has a label 164 | if(classToModify.getAnnotations(ontology, OWLRDFVocabulary.RDFS_LABEL.getURI()).size() == 0 ) 165 | { 166 | //we get the URI of the class and add it as label 167 | OWLAnnotation labelAnno = df.getOWLLabelAnnotation(classToModify.toString(), "en"); 168 | OWLAxiom ax = df.getOWLEntityAnnotationAxiom(classToModify, labelAnno); 169 | 170 | try { 171 | manager.applyChange(new AddAxiom(ontology, ax)); 172 | } catch (OWLOntologyChangeException e1) { 173 | e1.printStackTrace(); 174 | } 175 | } 176 | 177 | /* apply the changes */ 178 | try { 179 | manager.applyChanges(classRenamer.changeURI(toModify, uriName)); 180 | } catch (OWLOntologyChangeException e) { 181 | e.printStackTrace(); 182 | } 183 | //we add the newly assigned ID to the list of already used IDs 184 | listUsedIDs.add(uriName); 185 | } 186 | 187 | //if we want to check visually the list of IDs that are used 188 | /*for (Iterator it=listUsedIDs.iterator(); it.hasNext(); ) { 189 | System.out.println("used "+it.next()); 190 | }*/ 191 | 192 | 193 | /* time to wrap up and save the file */ 194 | try { 195 | manager.saveOntology(ontology, physicalURI2); 196 | 197 | 198 | } catch (UnknownOWLOntologyException e) { 199 | e.printStackTrace(); 200 | } catch (OWLOntologyStorageException e) { 201 | e.printStackTrace(); 202 | } 203 | 204 | 205 | 206 | 207 | } 208 | 209 | } 210 | -------------------------------------------------------------------------------- /src/tools/build/modify-uris.pl: -------------------------------------------------------------------------------- 1 | use strict; 2 | use File::Copy; 3 | # Rewrite the old OBI namespace into new purls. Beware UGLY HACKS below 4 | 5 | # Policy here. TBD. 6 | 7 | my $idNamespace = "http://purl.obofoundry.org/obo/"; # conservative, but less elegant: http://purl.org/obo/OBI/. Current OBO practice: http://purl.org/obo/OBI# 8 | my $namedclassNamespace = "http://purl.obofoundry.org/obo/"; 9 | my $propertyNamespace = "http://purl.obofoundry.org/obo/"; # can't stay at top level, since no OBI differentiation with OBI_ 10 | my $individualNamespace = "http://purl.obofoundry.org/obo/"; 11 | 12 | my $debug = 0; 13 | 14 | my $cwd=`pwd`; 15 | chop $cwd; 16 | my $trunk=$cwd."/".$0; 17 | $trunk=~s|/src/tools.*||; 18 | my $branches = "$trunk/src/ontology/branches"; 19 | my $external = "$trunk/src/ontology/external"; 20 | my $ontology = "$trunk/src/ontology"; 21 | my $build = "$trunk/build"; 22 | 23 | # suck in obi.owl to know which files to process 24 | # open TOP, "<$branches/obi.owl" or die("can't find obi.owl"); 25 | # my @lines = ; 26 | # close TOP; 27 | 28 | my $copydir = "$build/newids/"; # write the rewritten files here 29 | my $copyexternal = "$build/external/"; 30 | 31 | my %used; # to record used numeric ids 32 | 33 | # extract the names of the branches 34 | # my @obiParts = grep {/) 51 | { /(\S+)\s+(\S+)/; 52 | 53 | my ($type,$uri) = ($1,$2); 54 | 55 | my $rewrite = maybeRewriteURI($type,$uri); 56 | 57 | 58 | if (defined $rewrite) 59 | { if ($rewrite) 60 | { $uriReplacements{$uri}=$rewrite; } 61 | else { push @todo,$uri }; 62 | } 63 | else {$debug && print "don't bother ",$uri,"\n"} 64 | } 65 | close URILIST; 66 | foreach my $do (@todo) 67 | { 68 | my $newid = allocateNewId(); 69 | $uriReplacements{$do} = $idNamespace."IAO_".$newid; 70 | s/.*[\/#]//; 71 | $tagReplacements{$do}="IAO_".$newid; 72 | $debug && print $do,"=>",$uriReplacements{$do},"\n"; 73 | print $do,"=>",$uriReplacements{$do},"\n"; 74 | 75 | } 76 | } 77 | 78 | # Rewrite one URI Logic: 79 | # If we already are an OBI_\d+ then rewrite to $idNamespace but normalize to 7 digits with leading 0s and return new. 80 | # If we are a class and don't currently have an OBI_\d+, return 0. Caller will allocate new id. 81 | # If we are a property and not an OBI_\d+ then rewrite to $propertyNamespace and return new. 82 | # If we are an individual and not an OBI_\d+ then rewrite to $individualNamespace and return new. 83 | # Otherwise leave alone (return undef) 84 | 85 | sub maybeRewriteURI 86 | { my ($type,$uri) = @_; 87 | $debug && print "in: $type $uri\n"; 88 | if ($type =~ /Class|Property|Individual/) 89 | {if ($uri =~ /http:\/\/purl\.obofoundry\.org\/obo\/(.*)/) 90 | { my $localname = $1; 91 | if ( $localname =~ /IAO_(\d+)/) 92 | { if (length($1)>7) { return 0 } # too long - allocate new id 93 | my $newnum = sprintf("%07d",$1); 94 | if ($used{$newnum}) # collision, allocate new id 95 | { return 0 } 96 | else 97 | { $used{$newnum} = 1; 98 | return($idNamespace."IAO_".$newnum) 99 | } 100 | } 101 | # elsif ($localname =~ /CurationStatus|EnumerationClass/) 102 | # { return $namedclassNamespace.$localname } 103 | else 104 | { return(0) } 105 | } 106 | else {return undef} 107 | } 108 | elsif ($type =~ /Property/) 109 | {if ($uri =~ /http:\/\/purl\.obofoundry\.org\/obo\/(.*)/) 110 | { if ($1 =~ /IAO_\d+/) 111 | { $uri = $idNamespace.$1; } 112 | else 113 | { $uri = $propertyNamespace.$1 } 114 | } 115 | else 116 | { return (undef) } 117 | } 118 | elsif ($type =~ /Individual/) 119 | {if ($uri =~ /http:\/\/purl\.obofoundry\.org\/obo\/(.*)/) 120 | { if ($1 =~ /IAO_\d+/) 121 | { $uri = $idNamespace.$1; } 122 | else 123 | { $uri = $individualNamespace.$1 } 124 | } 125 | else 126 | { return (undef) } 127 | } 128 | } 129 | 130 | # Allocated a new id Logic: 131 | # Use the next numeric id that hasn't already been used. 132 | my $count=1; 133 | sub allocateNewId 134 | { my $test; 135 | for ($test = sprintf("%07d",$count); $used{$test}; $count++) {$test = sprintf("%07d",$count)} 136 | $used{$test}=1; 137 | $test; 138 | } 139 | 140 | sub replacenames 141 | { my $count=1; 142 | #foreach my $part ( @obiParts) { 143 | # my $path = "$branches/$part".".owl"; 144 | my $path = "$ontology/IAO.owl"; 145 | open PART, "<$path" or die("Trouble loading $path"); 146 | if (! -e $copydir) { mkdir($copydir,0777) }; 147 | # if (! -e "$copyexternal") { mkdir("$copyexternal",0777) }; 148 | # copy("$branches/obid.owl", "$copydir/obid.owl") or die("Couldn't copy obid.owl"); 149 | # foreach my $file qw(bfo11.owl ro.owl ro_bfo_bridge11.owl protege.owl protege-dc.owl) 150 | # { copy("$external/$file", "$copyexternal/$file") or die("Couldn't copy $file");} 151 | my $copypath = $copydir."IAO.owl"; 152 | open PARTCOPY, ">$copypath" or die ("Trouble writing $path"); 153 | my $copy; 154 | while () { 155 | s/\s*xmlns=.*/ xmlns="$propertyNamespace"/; 156 | s/\s*xmlns:obi=.*/ xmlns:obi="$idNamespace"/; 157 | s/\s*xml(ns){0,1}:(.+?)="http:\/\/obi.source.*\/(.*)/ xml$1:$2="$idNamespace\obi\/$3/; 158 | # Fix any text curation status 159 | my $pre = "curation_status>ready_for_releasemetadata_incompletemetadata_completeuncuratedpending_final_vettingdefinition_incomplete.*?