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Knowledge-Graph-Hub / kg-obo

A package to transform all OBO ontologies into KGX TSV format and OBO json, and put the transformed graph in KGhub
https://knowledge-graph-hub.github.io/kg-obo/getting_started.html
GNU General Public License v3.0
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Version for iceo parsed incorrectly #115

Closed caufieldjh closed 2 years ago

caufieldjh commented 2 years ago

Describe the bug

The version identifier for iceo is parsed incorrectly, leaving only a set of underscores (suggesting that the parsed value is only spaces and/or illegal chars). This is visible in the most recent test build:

18:18:50  iceo
18:18:50  http://purl.obolibrary.org/obo/iceo.owl
18:18:50  Current VersionIRI for iceo: http://purl.obolibrary.org/obo/2019/1/ICEO
18:18:50  Current version for iceo: 
18:18:50  ________
18:18:50  Don't have this version of iceo yet - will transform.
18:18:50  No imports found for iceo.

To Reproduce

python3 run.py --s3_test --bucket kg-test --get_only iceo

Expected behavior

The header for iceo contains:

...
    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/2019/1/ICEO">
        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">2.1</owl:versionInfo>
        <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string">01-14-2021</dc:date>
        <dc:description>A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning.</dc:description>
        <dc:creator>Meng LIU</dc:creator>
        <dc:title>ICEO: Ontology of Integrative and Conjugative Elements</dc:title>
        <rdfs:comment>The ICEO Ontology is licensed under CC BY 4.0.</rdfs:comment>
        <rdfs:isDefinedBy>Meng LIU</rdfs:isDefinedBy>
        <dc:subject>A biological ontology in the domain of Integrative and Conjugative Elements.</dc:subject>
        <dc:creator>Yongqun He</dc:creator>
        <terms:license>http://creativecommons.org/licenses/by/4.0/</terms:license>
        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This is an ICE ontology 2.1, representing the information of 271 experimentally verified ICEs from 235 bacterial strains and 311 putative ICEs from 272 Klebsiella pneumoniae.</rdfs:comment>
        <dc:creator>Hong-Yu Ou</dc:creator>
    </owl:Ontology>

The version for this OBO should be '2.1'.

Version

d8ef8798513472140b29a0738cbdacbbb67fcff3

caufieldjh commented 2 years ago

The same appears to happen for kisao:

13:34:19  kisao
13:34:19  http://purl.obolibrary.org/obo/kisao.owl
13:34:19  Current VersionIRI for kisao: http://www.biomodels.net/kisao/KISAO#
13:34:19  Current version for kisao: 
13:34:19  ________
13:34:19  Don't have this version of kisao yet - will transform.

kisao header:

...
    <owl:Ontology rdf:about="http://www.biomodels.net/kisao/KISAO#">
        <dc:rights>Artistic License 2.0</dc:rights>
        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/pubmed/22027554</rdfs:seeAlso>
        <rdfs:label xml:lang="en">Kinetic Simulation Algorithm Ontology (KiSAO)</rdfs:label>
        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">2.30</owl:versionInfo>
        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://co.mbine.org/standards/kisao</rdfs:seeAlso>
        <protege:defaultLanguage>en</protege:defaultLanguage>
        <skos:definition xml:lang="en">The Kinetic Simulation Algorithm Ontology (KiSAO) classifies algorithms available for the simulation and analysis of models in biology, and their characteristics and the parameters required for their use.</skos:definition>
        <rdfs:comment xml:lang="en">This is a core version which contains all but deprecated classes.</rdfs:comment>
    </owl:Ontology>