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[bioontology-support] [BioPortal] Feedback from VJHenry

Vincent Henry vincent643 at gmail.com
Tue Apr 21 09:26:31 PDT 2020


Hi Michael,

Thank you very much for your return.
You're right, it is a contact email address with "@" that was
misinterpreted.
I'll never find it by myself. I'll upload new files.

Best regards,
Vincent

On Tue, Apr 21, 2020 at 1:31 AM Michael Vladimir Dorf <mdorf at stanford.edu>
wrote:

> Hi Vincent,
>
> I’ve done some further troubleshooting of your ontologies, and some flags
> were raised by our tools in regards to their source:
>
> Although we can load the ontologies without errors (including in Protege),
> the second step in the parsing process fails when we attempt to serialize
> the data to ntriples format to load it into our RDF store:
>
> ▲ repository/BIPOM-CC-INF/1 ▶ rapper -i ntriples -c data.triples
> rapper: Parsing URI
> file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples with parser
> ntriples
> rapper: Error - URI
> file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples:2 column
> 2531 - Junk after terminating "."
> rapper: Error - URI
> file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples:9647 column
> 2561 - Junk after terminating “."
>
> Both of these errors refer to a comment that appears inside ALL of your
> ontology source files. The NTriples file refers to this section of code:
>
> <http://purl.obolibrary.org/obo/BiPOm> <http://www.w3.org/2000/01/rdf-schema#comment> "BiPOm\n\n1. Copyright of ontology\n\nThe ontology was created jointly by the BioSys group at the research unit of Applied mathematics and computer science  \nfrom genomes to the environment (MaIAGE) of the Institut National de la Recherche Agronomique (INRA) France, by the group the Large-scale Heterogeneous DAta and Knowledge (LaHDAK team) of the Laboratoire de recherche en informatique (LRI) of the Universit\u00E9 Paris-Sud/CNRS, France  and by the D\u00E9partement MMIP AgroParisTech of the INRA, France.\nINRA, Agroparistech and  Universit\u00E9 Paris-Sud own the copyright of the ontology BiPOm. \n\n2. License terms\n\nThe ontology BiPOm is licensed under the Creative Commons\nAttribution 4.0 Unported (CC BY 4.0) license. To view a\ncopy of this license, visit http://creativecommons.org/licenses/by/4.0/\nor send a letter to Creative Commons, 444 Castro Street, Suite 900,\nMountain View, California, 94041, USA.   \n\n\n3. Notice\nThis product contains references to classes of the Gene Ontology (GO) (http://geneontology.org/) developed by the Gene Ontology consortium, \nlicensed under the terms Creative Commons Attribution 4.0 Unported license (https://creativecommons.org/licenses/by/4.0/).\n\nThis product contains references to classes of the Chemical Entities of Biological Interest (ChEBI) (https://www.ebi.ac.uk/chebi/init.do) developed by the ChEBI consortium. \n\nThis product contains references to classes of the Sequence Ontology (SO) (http://www.sequenceontology.org/) developed by the SO consortium and are freely reusable. \n\nThis product contains references to classes of the Systems Biology Ontology (SBO)  (http://www.ebi.ac.uk/sbo/main/) developed by the SBO consortium, \nlicensed under the terms of Artistic License 2.0 (https://opensource.org/licenses/artistic-license-2.0.php).\n\nThis product contains references to properties of the Relation Ontology (RO)  (http://www.obofoundry.org/ontology/ro.html) developed by the OBO foundry, \nlicensed under the terms Creative Commons Attribution 3.0 Unported License (https://creativecommons.org/licenses/by/3.0/).\n\nThis product contains references to properties of the Basic Formal Ontology (BFO)  (http://ifomis.uni-saarland.de/bfo/) developed by the BFO consortium,\n licensed under the terms Creative Commons Attribution 3.0 Unported License (https://creativecommons.org/licenses/by/3.0/).\n\n4. Contact\nFor questions and remarks concerning BiPOm:\nAnne Goelzer\nAnne.Goelzer"@inra.fr .
>
> Below is the original source code corresponding to this triple:
>
> <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BiPOm">
> <rdfs:comment xml:lang="inra.fr">BiPOm
>
> 1. Copyright of ontology
>
> The ontology was created jointly by the BioSys group at the research unit of Applied mathematics and computer science
> from genomes to the environment (MaIAGE) of the Institut National de la Recherche Agronomique (INRA) France, by the group the Large-scale Heterogeneous DAta and Knowledge (LaHDAK team) of the Laboratoire de recherche en informatique (LRI) of the Université Paris-Sud/CNRS, France  and by the Département MMIP AgroParisTech of the INRA, France.
>
> ***************** SNIP *****************
>
>     4. Contact
> For questions and remarks concerning BiPOm:
>                                          Anne Goelzer
> Anne.Goelzer</rdfs:comment>
>     </rdf:Description>
>
> I am not an ontology development expert to point to the exact issue with
> this code, but both my colleague and I think that the language definition
> is incorrect:
>
> <rdfs:comment xml:lang="inra.fr">
>
>
> The expectation is to see something like xml:lang="en" or xml:lang=“fr"
>
> I’d recommend correcting this entry and adding a new submission of your
> ontology(ies). Also, please let us know which ontologies need to be deleted
> so as to address the incorrect acronym issue.
>
> Thank you,
>
> Michael
>
>
> ----------------------------------------------------
> Michael Dorf
> Chief Software Architect
> The National Center for Biomedical Ontology
> Stanford Biomedical Informatics Research
> mdorf at stanford.edu
> O: 650-723-0357
> M: 650-995-4374
> ----------------------------------------------------
>
> On Apr 19, 2020, at 1:41 PM, John Graybeal <jgraybeal at stanford.edu> wrote:
>
> Hi Vincent,
>
> Here are some quick replies for now, please respond with whatever issues
> remain.
>
> - the creation of "BiPOm-RPCC-instanciated" (
> https://bioportal.bioontology.org/ontologies/BIPOM-INST)
>
> If you are asking to have this deleted, we can do that. Please confirm
> that is what you want.
>
> - the description of "BiPOm inferences for Calvin cycle" (
> https://bioportal.bioontology.org/ontologies/BIPOM-CC-INF) followed
> instead of following
>
> Descriptions can be modified by you; click on the pencil icon to edit the
> ontology metadata (at upper right) or the submission metadata (above the
> submission list).
>
> - the acronym of "BiPOm E-Coli metabolism instantiation" (
> https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INF)
> BIPOM-ECMET-INST instead of BIPOM-ECMET-INF
> and the the acronym of "BiPOm inferences for E-Coli metabolism" (
> https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INFF)
> BIPOM-ECMET-INF instead of BIPOM-ECMET-INFF.
>
> Acronyms can not be changed they are the index for everything in the
> system. To make this happen, you will need to re-submit your ontology(ies)
> under the new acronym you want to use, then tell us to delete the original
> ontology(ies). Unfortunately the history will be lost.
>
> Finally I'm wondering why my recent uploads are mentioned as "Error Rdf" ?
>
> I don't have time to look at the details at this moment, but the best way
> to figure this out is to try loading the ontology in Protege. If it is not
> parseable in BioPortal (which is what this indicates), it is almost always
> not parseable in Protege, for the same reasons because they use the same
> parser. And Protege actually shows you the errors, which makes it a much
> better tool for finding and fixing issues.
>
> Hope this helps!
>
> John
>
>
> On Apr 18, 2020, at 6:25 AM, support at bioontology.org wrote:
>
> Name: VJHenry
>
> Email: vincent643 at gmail.com <vincent643 at gmail.com>
>
> Location: https%3A%2F%2Fbioportal.bioontology.org
> <http://2fbioportal.bioontology.org/>%2Fontologies%2FBIPOM-CC-INF
>
>
> *Feedback:*
>
> Hi,
> I'm wondering if its possible to change some mistakes I made:
> - the creation of "BiPOm-RPCC-instanciated" (
> https://bioportal.bioontology.org/ontologies/BIPOM-INST)
> - the description of "BiPOm inferences for Calvin cycle" (
> https://bioportal.bioontology.org/ontologies/BIPOM-CC-INF) followed
> instead of following
> - the acronym of "BiPOm E-Coli metabolism instantiation" (
> https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INF)
> BIPOM-ECMET-INST instead of BIPOM-ECMET-INF
> and the the acronym of "BiPOm inferences for E-Coli metabolism" (
> https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INFF)
> BIPOM-ECMET-INF instead of BIPOM-ECMET-INFF.
>
> Finally I'm wondering why my recent uploads are mentioned as "Error Rdf" ?
>
> Thank you very much for all,
> Best regards,
> Vincent (VJHenry; vincent643 at gmail.com)
>
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> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
> ========================
> John Graybeal
> Technical Program Manager
> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
> 650-736-1632  | ORCID  0000-0001-6875-5360
>
>
>
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> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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>
>
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