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[bioontology-support] [BioPortal] Feedback from Kellie Fay

Michael Dorf mdorf at stanford.edu
Wed Oct 4 11:41:17 PDT 2017


Hi Kellie,

The screenshot you posted appears to be a view of the term “umbilicus” from the Neuroscience Information Framework Standard Ontology (NIFSTD). Here is the link:

http://bioportal.bioontology.org/ontologies/NIFSTD?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0007118<http://bioportal.bioontology.org/ontologies/NIFSTD?p=classes&conceptid=http://purl.obolibrary.org/obo/UBERON_0007118>

A corresponding REST API call is:

http://data.bioontology.org/ontologies/NIFSTD/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0007118?display=all<http://data.bioontology.org/ontologies/NIFSTD/classes/http://purl.obolibrary.org/obo/UBERON_0007118?display=all>

This ontology happens to define a property called “database_cross_reference”, which is populated with the alternative terms. I believe that the actual “source” ontology of this term is Uber Anatomy Ontology (UBERON). It appears to have a slightly better coverage for the same term (and the “database_cross_reference” property is also defined):

http://bioportal.bioontology.org/ontologies/UBERON?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0007118<http://bioportal.bioontology.org/ontologies/UBERON?p=classes&conceptid=http://purl.obolibrary.org/obo/UBERON_0007118>

A corresponding REST API call is:

http://data.bioontology.org/ontologies/UBERON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0007118?display=all<http://data.bioontology.org/ontologies/UBERON/classes/http://purl.obolibrary.org/obo/UBERON_0007118?display=all>


Unfortunately, “database_cross_reference” isn’t a required attribute, and based on my quick review of the same term defined in different ontologies, most of them either don’t define it or have alternate properties for cross-referencing:

http://bioportal.bioontology.org/ontologies/MESH?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD014472<http://bioportal.bioontology.org/ontologies/MESH?p=classes&conceptid=http://purl.bioontology.org/ontology/MESH/D014472>
http://bioportal.bioontology.org/ontologies/FMA?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fsig%2Font%2Ffma%2Ffma61584<http://bioportal.bioontology.org/ontologies/FMA?p=classes&conceptid=http://purl.org/sig/ont/fma/fma61584>
http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C77533<http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C77533>

I think, based on your requirements, exploring mappings is still your best bet:

http://data.bioontology.org/ontologies/UBERON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0007118/mappings<http://data.bioontology.org/ontologies/UBERON/classes/http://purl.obolibrary.org/obo/UBERON_0007118/mappings>

If “database_cross_reference” is your preferred property, you can always iterate over the list of our ontologies and examine properties for each, noting those that contain the “database_cross_reference”. An API call for this is:

http://data.bioontology.org/ontologies/UBERON/properties
http://data.bioontology.org/ontologies/UBERON/properties/http%3A%2F%2Fwww.geneontology.org%2Fformats%2FoboInOwl%23hasDbXref<http://data.bioontology.org/ontologies/UBERON/properties/http://www.geneontology.org/formats/oboInOwl#hasDbXref>

Hope this helps. We’ll be happy to offer further assistance if this doesn’t do the trick!

Thanks!

Michael



On Oct 4, 2017, at 7:57 AM, Fay, Kellie <Fay.Kellie at epa.gov<mailto:Fay.Kellie at epa.gov>> wrote:

Thanks Michael.  I am not so interested in all of the mappings within a given ontology, but I would like to quickly obtain ALL alternate ontology mappings for a given class (and its synonyms).  In my “navel” example, when I queried it last week on the annotator page, several matching ontologies were returned.  Any of those linked to a mapping page (e.g., the first link you provided below) provided not only the ontology ID for that particular ontology (e.g., FMA)  but also had a field “database_cross_reference”, containing alternative ontology IDs  (e.g., for navel: UMLS, galen, GAID, MeSH).  This is no longer provided on the mapping page that I can see.  It is possible I’m confused, but I went through this example last week with a team and we all have notes that this worked, plus a screenshot:
 [cid:AC855C81-BBA8-4411-ADD4-6B3128EB3EEC at stanford.edu]


Eventually, our goal is to obtain all possible ontology IDs for a large batch of terms (classes) and we would like to use BioPortal to access these.  This area is not my expertise, but one of my colleagues is looking to develope code so that we can map thousands of our terms across your different ontologies.  I am guessing that database_cross_reference  will be a key component.  If you have any expert advice on the best way to accomplish what we need, I certainly welcome your help.

Thank you and best regards,
Kellie

Kellie Fay, PhD
Research Scientist Senior, EPA SMAVCS3 Contract
Science and Engineering, CSRA Inc.

6201 Congdon Blvd, Suite 140, Duluth, MN 55804
T: 218-529-5159│F: 218-529-5003│ Fay.Kellie at epa.gov<mailto:Fay.Kellie at epa.gov>

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From: Michael Dorf [mailto:mdorf at stanford.edu]
Sent: Tuesday, October 03, 2017 5:28 PM
To: support at bioontology.org<mailto:support at bioontology.org>
Cc: Fay, Kellie <Fay.Kellie at epa.gov>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Kellie Fay

Hi Kellie,

Thank you for writing to us. Are you possibly referring to the mappings page that displays the alternate classes in different ontologies that are mapped to the given class? For your “Umbilicus/Navel” example, the link would be:

https://bioportal.bioontology.org/ontologies/FMA?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fsig%2Font%2Ffma%2Ffma61584#mappings<https://bioportal.bioontology.org/ontologies/FMA?p=classes&conceptid=http://purl.org/sig/ont/fma/fma61584#mappings>

If you are looking for this info programmatically, you can use this REST service:

http://data.bioontology.org/ontologies/FMA/classes/http%3A%2F%2Fpurl.org%2Fsig%2Font%2Ffma%2Ffma61584/mappings<http://data.bioontology.org/ontologies/FMA/classes/http:/purl.org/sig/ont/fma/fma61584/mappings>

For a full list of mappings for a particular ontology, you can use the link below:

https://bioportal.bioontology.org/mappings

Thanks again, and let us know if you have further questions.

Michael


On Oct 1, 2017, at 8:30 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Kellie Fay
Email: fay.kellie at epa.gov<mailto:fay.kellie at epa.gov>
Location: https%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FFMA%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.org<http://252fpurl.org/>%252Fsig%252Font%252Ffma%252Ffma61584

Feedback:
I am interested in cross referencing IDs in various ontologies for the same class. Perhaps I am mistaken, but I believe last week a query on the annotator page returned links to different ontologies that, when the link was opened, also displayed alternate ontology IDs for the queried class. I do not see that the alternate IDs are provided easily any longer. Please correct me if I am wrong! I used the example of "navel" and was able to quickly see that their were relevant IDs for UMLS, FMA, galen and MeSH. Not so easy to find now...

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