diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 879cd04..491d480 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -10,7 +10,7 @@ # More information: https://github.com/INCATools/ontology-development-kit/ # Fingerprint of the configuration file when this Makefile was last generated -CONFIG_HASH= 063948980a77d2cae11b525e208d573c79ba7ada9bb786ef8519bf6438fdc969 +CONFIG_HASH= 6bdc85a714f6ee8c03d73f3362a5362d0fe4354c253f35c4f4b4b4d4482f0e4a # ---------------------------------------- @@ -455,8 +455,8 @@ mirror-iao: | $(TMPDIR) .PHONY: mirror-obi .PRECIOUS: $(MIRRORDIR)/obi.owl mirror-obi: | $(TMPDIR) - curl -L $(OBOBASE)/obi/obi-base.owl --create-dirs -o $(TMPDIR)/obi-download.owl --retry 4 --max-time 200 && \ - $(ROBOT) convert -i $(TMPDIR)/obi-download.owl -o $(TMPDIR)/$@.owl + curl -L $(OBOBASE)/obi.owl --create-dirs -o $(TMPDIR)/obi-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) remove -i $(TMPDIR)/obi-download.owl --base-iri $(OBOBASE)/OBI --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl ## ONTOLOGY: chebi diff --git a/src/ontology/imports/obi_import.owl b/src/ontology/imports/obi_import.owl index 6c209d5..6ee6ddd 100644 --- a/src/ontology/imports/obi_import.owl +++ b/src/ontology/imports/obi_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2024-08-19") + +Annotation( ) +Annotation(owl:versionInfo "2024-08-21") Declaration(Class()) Declaration(Class()) @@ -17,6 +17,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -33,6 +34,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -67,6 +69,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -169,6 +172,7 @@ AnnotationAssertion( "has_specified_input"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) +ObjectPropertyDomain( ) # Object Property: (is_specified_input_of) @@ -180,6 +184,7 @@ AnnotationAssertion( "PERSON:Bjoern Peters") AnnotationAssertion(rdfs:label "is_specified_input_of"@en) SubObjectPropertyOf( ) +ObjectPropertyRange( ) # Object Property: (has_specified_output) @@ -193,6 +198,7 @@ AnnotationAssertion( "has_specified_output"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) +ObjectPropertyDomain( ) # Object Property: (is_specified_output_of) @@ -203,17 +209,20 @@ AnnotationAssertion( "PERSON:Bjoern Peters") AnnotationAssertion(rdfs:label "is_specified_output_of"@en) SubObjectPropertyOf( ) +ObjectPropertyRange( ) # Object Property: (achieves_planned_objective) AnnotationAssertion( "achieves_planned_objective") AnnotationAssertion( "A cell sorting process achieves the objective specification 'material separation objective'") +AnnotationAssertion( ) AnnotationAssertion( "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.") AnnotationAssertion( "BP, AR, PPPB branch") AnnotationAssertion( "PPPB branch derived") AnnotationAssertion( "modified according to email thread from 1/23/09 in accordince with DT and PPPB branch") AnnotationAssertion(rdfs:label "achieves_planned_objective") InverseObjectProperties( ) +ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (objective_achieved_by) @@ -225,6 +234,7 @@ AnnotationAssertion( "OBI") AnnotationAssertion(rdfs:label "objective_achieved_by") ObjectPropertyDomain( ) +ObjectPropertyRange( ) @@ -232,9 +242,21 @@ ObjectPropertyDomain( () - -AnnotationAssertion( "human being") +# Class: (planned process) + +AnnotationAssertion( "planned process") +AnnotationAssertion( "Injecting mice with a vaccine in order to test its efficacy") +AnnotationAssertion( ) +AnnotationAssertion( "A process that realizes a plan which is the concretization of a plan specification."@en) +AnnotationAssertion( "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)") +AnnotationAssertion( "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some +objectives is a planned process.") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "branch derived") +AnnotationAssertion( "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)"@en) +AnnotationAssertion( "6/11/9: Edited at workshop. Used to include: is initiated by an agent") +AnnotationAssertion(rdfs:label "planned process"@en) +SubClassOf( ) # Class: (processed material) @@ -245,6 +267,7 @@ AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) AnnotationAssertion(rdfs:label "processed material"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) # Class: (material processing) @@ -261,7 +284,7 @@ AnnotationAssertion( "OBI branch derived"@en) AnnotationAssertion(rdfs:label "material processing"@en) EquivalentClasses( ObjectSomeValuesFrom( )) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectAllValuesFrom( )) @@ -457,7 +480,7 @@ AnnotationAssertion( "http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400014") AnnotationAssertion( "NMR instrument") AnnotationAssertion(rdfs:label "NMR probe") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -473,6 +496,16 @@ AnnotationAssertion( "flow probe") SubClassOf( ) +# Class: (vial) + +AnnotationAssertion( "vial") +AnnotationAssertion( ) +AnnotationAssertion( "A container made from solid material and primarily used for holding liquid.") +AnnotationAssertion( "https://orcid.org/0000-0002-8844-9165") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Vial") +AnnotationAssertion(rdfs:label "vial") +SubClassOf( ) + # Class: (magic angle spinning rotor) AnnotationAssertion( "magic angle spinning rotor") @@ -646,7 +679,7 @@ AnnotationAssertion( "http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400059") AnnotationAssertion( "NMR instrument") AnnotationAssertion(rdfs:label "NMR instrument") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (manufacturer role) @@ -896,6 +929,18 @@ AnnotationAssertion( "JEOL ECA NMR spectrometer") SubClassOf( ) +# Class: (measurement device) + +AnnotationAssertion( "measurement device") +AnnotationAssertion( "A ruler, a microarray scanner, a Geiger counter.") +AnnotationAssertion( ) +AnnotationAssertion( "A device in which a measure function inheres.") +AnnotationAssertion( "GROUP:OBI Philly workshop") +AnnotationAssertion( "OBI") +AnnotationAssertion(rdfs:label "measurement device") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + # Class: (manufacturer) AnnotationAssertion( "manufacturer") @@ -915,7 +960,7 @@ AnnotationAssertion( "sample tube") AnnotationAssertion( "http://en.wikipedia.org/wiki/Test_tube") AnnotationAssertion(rdfs:label "test tube") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (container) @@ -927,6 +972,7 @@ AnnotationAssertion( "PERSON: Bjoern Peters") AnnotationAssertion(rdfs:label "container") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) # Class: (device) @@ -950,7 +996,7 @@ AnnotationAssertion( "instrument") AnnotationAssertion( "OBI development call 2012-12-17.") AnnotationAssertion(rdfs:label "device") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -980,6 +1026,7 @@ SubClassOf( (Thermo) AnnotationAssertion( "Thermo") +AnnotationAssertion( ) AnnotationAssertion( "Philippe Rocca-Serra") AnnotationAssertion(rdfs:label "Thermo") ClassAssertion( ) @@ -987,6 +1034,7 @@ ClassAssertion( (Waters) AnnotationAssertion( "Waters") +AnnotationAssertion( ) AnnotationAssertion( "Philippe Rocca-Serra") AnnotationAssertion(rdfs:label "Waters") ClassAssertion( ) @@ -994,6 +1042,7 @@ ClassAssertion( (BIO-RAD) AnnotationAssertion( "BIO-RAD") +AnnotationAssertion( ) AnnotationAssertion( "Philippe Rocca-Serra") AnnotationAssertion(rdfs:label "BIO-RAD") ClassAssertion( ) @@ -1001,6 +1050,7 @@ ClassAssertion( (Ambion) AnnotationAssertion( "Ambion") +AnnotationAssertion( ) AnnotationAssertion( "Philippe Rocca-Serra") AnnotationAssertion(rdfs:label "Ambion") ClassAssertion( ) @@ -1008,6 +1058,7 @@ ClassAssertion( (Helicos) AnnotationAssertion( "Helicos") +AnnotationAssertion( ) AnnotationAssertion( "Philippe Rocca-Serra") AnnotationAssertion(rdfs:label "Helicos") ClassAssertion( ) @@ -1015,6 +1066,7 @@ ClassAssertion( (Roche) AnnotationAssertion( "Roche") +AnnotationAssertion( ) AnnotationAssertion( "Philippe Rocca-Serra") AnnotationAssertion(rdfs:label "Roche") ClassAssertion( ) @@ -1022,6 +1074,7 @@ ClassAssertion( (Illumina) AnnotationAssertion( "Illumina") +AnnotationAssertion( ) AnnotationAssertion( "Philippe Rocca-Serra") AnnotationAssertion(rdfs:label "Illumina") ClassAssertion( ) @@ -1029,6 +1082,7 @@ ClassAssertion( (Agilent) AnnotationAssertion( "Agilent") +AnnotationAssertion( ) AnnotationAssertion( "Philippe Rocca-Serra") AnnotationAssertion(rdfs:label "Agilent") ClassAssertion( ) @@ -1036,6 +1090,7 @@ ClassAssertion( (Li-Cor) AnnotationAssertion( "Li-Cor") +AnnotationAssertion( ) AnnotationAssertion( "Philippe Rocca-Serra") AnnotationAssertion(rdfs:label "Li-Cor") ClassAssertion( ) @@ -1043,6 +1098,7 @@ ClassAssertion( (Bruker Corporation) AnnotationAssertion( "Bruker Corporation") +AnnotationAssertion( ) AnnotationAssertion( "Philippe Rocca-Serra") AnnotationAssertion(rdfs:label "Bruker Corporation") ClassAssertion( ) @@ -1050,6 +1106,7 @@ ClassAssertion( (Applied Biosystems) AnnotationAssertion( "Applied Biosystems") +AnnotationAssertion( ) AnnotationAssertion( "Philippe Rocca-Serra") AnnotationAssertion(rdfs:label "Applied Biosystems") ClassAssertion( ) @@ -1057,6 +1114,7 @@ ClassAssertion( (Bruker Daltonics) AnnotationAssertion( "Bruker Daltonics") +AnnotationAssertion( ) AnnotationAssertion( "Philippe Rocca-Serra") AnnotationAssertion(rdfs:label "Bruker Daltonics") ClassAssertion( ) @@ -1072,6 +1130,7 @@ ClassAssertion( (eBioscience) AnnotationAssertion( "eBioscience") +AnnotationAssertion( ) AnnotationAssertion( "Karin Breuer") AnnotationAssertion( "WEB:http://www.ebioscience.com/@2011/04/11") AnnotationAssertion(rdfs:label "eBioscience") @@ -1080,6 +1139,7 @@ ClassAssertion( (Cytopeia) AnnotationAssertion( "Cytopeia") +AnnotationAssertion( ) AnnotationAssertion( "Karin Breuer") AnnotationAssertion( "WEB:http://www.cytopeia.com/@2011/04/11") AnnotationAssertion(rdfs:label "Cytopeia") @@ -1088,6 +1148,7 @@ ClassAssertion( (Exalpha Biological) AnnotationAssertion( "Exalpha Biological") +AnnotationAssertion( ) AnnotationAssertion( "Karin Breuer") AnnotationAssertion( "WEB:http://www.exalpha.com/@2011/04/11") AnnotationAssertion(rdfs:label "Exalpha Biological") @@ -1096,6 +1157,7 @@ ClassAssertion( (Apogee Flow Systems) AnnotationAssertion( "Apogee Flow Systems") +AnnotationAssertion( ) AnnotationAssertion( "Karin Breuer") AnnotationAssertion( "WEB:http://www.apogeeflow.com/@2011/04/11") AnnotationAssertion(rdfs:label "Apogee Flow Systems") @@ -1104,6 +1166,7 @@ ClassAssertion( (Exbio Antibodies) AnnotationAssertion( "Exbio Antibodies") +AnnotationAssertion( ) AnnotationAssertion( "Karin Breuer") AnnotationAssertion( "WEB:http://www.exbio.cz/@2011/04/11") AnnotationAssertion(rdfs:label "Exbio Antibodies") @@ -1112,6 +1175,7 @@ ClassAssertion( (Becton Dickinson (BD Biosciences)) AnnotationAssertion( "Becton Dickinson (BD Biosciences)") +AnnotationAssertion( ) AnnotationAssertion( "Karin Breuer") AnnotationAssertion( "WEB:http://www.bdbiosciences.com/@2011/04/11") AnnotationAssertion(rdfs:label "Becton Dickinson (BD Biosciences)") @@ -1120,6 +1184,7 @@ ClassAssertion( (Dako Cytomation) AnnotationAssertion( "Dako Cytomation") +AnnotationAssertion( ) AnnotationAssertion( "Karin Breuer") AnnotationAssertion( "WEB:http://www.dakousa.com/@2011/04/11") AnnotationAssertion(rdfs:label "Dako Cytomation") @@ -1128,6 +1193,7 @@ ClassAssertion( (Millipore) AnnotationAssertion( "Millipore") +AnnotationAssertion( ) AnnotationAssertion( "Karin Breuer") AnnotationAssertion( "WEB:http://www.guavatechnologies.com/@2011/04/11") AnnotationAssertion(rdfs:label "Millipore") @@ -1136,6 +1202,7 @@ ClassAssertion( (Antigenix) AnnotationAssertion( "Antigenix") +AnnotationAssertion( ) AnnotationAssertion( "Karin Breuer") AnnotationAssertion( "WEB:http://www.antigenix.com/@2011/04/11") AnnotationAssertion(rdfs:label "Antigenix") @@ -1144,6 +1211,7 @@ ClassAssertion( (Partec) AnnotationAssertion( "Partec") +AnnotationAssertion( ) AnnotationAssertion( "Karin Breuer") AnnotationAssertion( "WEB:http://www.partec.de/@2011/04/11") AnnotationAssertion(rdfs:label "Partec") @@ -1152,6 +1220,7 @@ ClassAssertion( (Beckman Coulter) AnnotationAssertion( "Beckman Coulter") +AnnotationAssertion( ) AnnotationAssertion( "Karin Breuer") AnnotationAssertion( "WEB:http://www.beckmancoulter.com/@2011/04/11") AnnotationAssertion(rdfs:label "Beckman Coulter") @@ -1160,6 +1229,7 @@ ClassAssertion( (Advanced Instruments Inc. (AI Companies)) AnnotationAssertion( "Advanced Instruments Inc. (AI Companies)") +AnnotationAssertion( ) AnnotationAssertion( "Karin Breuer") AnnotationAssertion( "WEB:http://www.aicompanies.com/@2011/04/11") AnnotationAssertion(rdfs:label "Advanced Instruments Inc. (AI Companies)") @@ -1168,6 +1238,7 @@ ClassAssertion( (Miltenyi Biotec) AnnotationAssertion( "Miltenyi Biotec") +AnnotationAssertion( ) AnnotationAssertion( "Karin Breuer") AnnotationAssertion( "WEB:http://www.miltenyibiotec.com/@2011/04/11") AnnotationAssertion(rdfs:label "Miltenyi Biotec") @@ -1176,6 +1247,7 @@ ClassAssertion( (AES Chemunex) AnnotationAssertion( "AES Chemunex") +AnnotationAssertion( ) AnnotationAssertion( "Karin Breuer") AnnotationAssertion( "WEB:http://www.aeschemunex.com/@2011/04/11") AnnotationAssertion(rdfs:label "AES Chemunex") @@ -1184,6 +1256,7 @@ ClassAssertion( (Bentley Instruments) AnnotationAssertion( "Bentley Instruments") +AnnotationAssertion( ) AnnotationAssertion( "Karin Breuer") AnnotationAssertion( "WEB:http://bentleyinstruments.com/@2011/04/11") AnnotationAssertion(rdfs:label "Bentley Instruments") @@ -1192,6 +1265,7 @@ ClassAssertion( (Invitrogen) AnnotationAssertion( "Invitrogen") +AnnotationAssertion( ) AnnotationAssertion( "Karin Breuer") AnnotationAssertion( "WEB:http://www.invitrogen.com/@2011/04/11") AnnotationAssertion(rdfs:label "Invitrogen") @@ -1200,6 +1274,7 @@ ClassAssertion( (Luminex) AnnotationAssertion( "Luminex") +AnnotationAssertion( ) AnnotationAssertion( "Karin Breuer") AnnotationAssertion( "WEB:http://www.luminexcorp.com/@2011/04/11") AnnotationAssertion(rdfs:label "Luminex") @@ -1208,6 +1283,7 @@ ClassAssertion( (CytoBuoy) AnnotationAssertion( "CytoBuoy") +AnnotationAssertion( ) AnnotationAssertion( "Karin Breuer") AnnotationAssertion( "WEB:http://www.cytobuoy.com/@2011/04/11") AnnotationAssertion(rdfs:label "CytoBuoy") @@ -1216,6 +1292,7 @@ ClassAssertion( (Nimblegen) AnnotationAssertion( "Nimblegen") +AnnotationAssertion( ) AnnotationAssertion( "An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing.") AnnotationAssertion( "Person: Jie Zheng") AnnotationAssertion(rdfs:label "Nimblegen") @@ -1224,6 +1301,7 @@ ClassAssertion( (Pacific Biosciences) AnnotationAssertion( "Pacific Biosciences") +AnnotationAssertion( ) AnnotationAssertion( "An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution.") AnnotationAssertion( "Person: Jie Zheng") AnnotationAssertion(rdfs:label "Pacific Biosciences") @@ -1232,6 +1310,7 @@ ClassAssertion( (NanoString Technologies) AnnotationAssertion( "NanoString Technologies") +AnnotationAssertion( ) AnnotationAssertion( "An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules.") AnnotationAssertion(rdfs:label "NanoString Technologies") ClassAssertion( ) @@ -1239,6 +1318,7 @@ ClassAssertion( (Thermo Fisher Scientific) AnnotationAssertion( "Thermo Fisher Scientific") +AnnotationAssertion( ) AnnotationAssertion( "An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific.") AnnotationAssertion( "Chris Stoeckert, Helena Ellis") AnnotationAssertion( "https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific") @@ -1248,6 +1328,7 @@ ClassAssertion( (Oxford Nanopore Technologies) AnnotationAssertion( "Oxford Nanopore Technologies") +AnnotationAssertion( ) AnnotationAssertion( "An organization that is developing and selling nanopore sequencing products and is based in the UK.") AnnotationAssertion( "James A. Overton") AnnotationAssertion( "https://en.wikipedia.org/wiki/Oxford_Nanopore_Technologies") @@ -1257,6 +1338,7 @@ ClassAssertion( (BioGents) AnnotationAssertion( "BioGents") +AnnotationAssertion( ) AnnotationAssertion( "An organization that manufactures mosquito traps and other mosquito control products.") AnnotationAssertion( "John Judkins") AnnotationAssertion( "WEB:https://eu.biogents.com/about-biogents/") @@ -1266,6 +1348,7 @@ ClassAssertion( (Abbott) AnnotationAssertion( "Abbott") +AnnotationAssertion( ) AnnotationAssertion( "A manufacturer of rapid point-of-care assay devices.") AnnotationAssertion( "John Judkins ORCID:0000-0001-6595-0902") AnnotationAssertion( "WEB:https://www.globalpointofcare.abbott/en/about.html") @@ -1276,6 +1359,7 @@ ClassAssertion( (J. Mitra) AnnotationAssertion( "J. Mitra") +AnnotationAssertion( ) AnnotationAssertion( "A manufacturer of in vitro diagnostic assay kits in India.") AnnotationAssertion( "John Judkins ORCID:0000-0001-6595-0902") AnnotationAssertion( "WEB:https://jmitra.co.in/about-us/") @@ -1286,6 +1370,7 @@ ClassAssertion( (InBios) AnnotationAssertion( "InBios") +AnnotationAssertion( ) AnnotationAssertion( "A manufacturer that specializes in in vitro diagnostic devices designed to test for infectious diseases.") AnnotationAssertion( "John Judkins ORCID:0000-0001-6595-0902") AnnotationAssertion( "WEB:https://inbios.com/about/") diff --git a/src/ontology/imports/obi_remove_list.txt b/src/ontology/imports/obi_remove_list.txt index 4ecd7f5..e577581 100644 --- a/src/ontology/imports/obi_remove_list.txt +++ b/src/ontology/imports/obi_remove_list.txt @@ -10,7 +10,6 @@ OBI:0000684 # 'specimen collection objective' OBI:0001933 # 'value specification' OBI:0000017 # 'regulatory role' OBI:0000947 # 'service provider role' -OBI:0000832 # 'measurement device' OBI:0002989 # 'material supplier' OBI:0000450 # 'regulatory agency' IAO:0000009 diff --git a/src/ontology/nmrCV-odk.yaml b/src/ontology/nmrCV-odk.yaml index 6bc6a1f..b775ac5 100644 --- a/src/ontology/nmrCV-odk.yaml +++ b/src/ontology/nmrCV-odk.yaml @@ -32,7 +32,6 @@ robot_java_args: '-Xmx16G' # max RAM to be used by Robot in ODK use_templates: TRUE -## NMR specific Settings ## import_group: products: @@ -46,7 +45,7 @@ import_group: #- id: chmo #- id: pato - id: obi - use_base: true + make_base: true module_type: custom - id: chebi is_large: true diff --git a/src/ontology/nmrCV.Makefile b/src/ontology/nmrCV.Makefile index 6c77ea6..e7e4205 100644 --- a/src/ontology/nmrCV.Makefile +++ b/src/ontology/nmrCV.Makefile @@ -10,7 +10,7 @@ $(IMPORTDIR)/obi_import.owl: $(MIRRORDIR)/obi.owl $(IMPORTDIR)/obi_terms.txt if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ - extract -T $(IMPORTDIR)/obi_terms.txt --force true --copy-ontology-annotations true --individuals minimal --intermediates minimal --method BOT \ + extract -T $(IMPORTDIR)/obi_terms.txt --force true --copy-ontology-annotations true --individuals minimal --method BOT \ query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ remove -T $(IMPORTDIR)/obi_remove_list.txt --select "self descendants instances" --signature true \ $(ANNOTATE_CONVERT_FILE); fi \ No newline at end of file