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[bioontology-support] [BioPortal] Feedback from Philip van Damme

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue Apr 28 11:56:44 PDT 2020


Hello Philip,


On Apr 9, 2020, at 2:35 AM, Damme, P. van (Philip) <p.vandamme at amsterdamumc.nl<mailto:p.vandamme at amsterdamumc.nl>> wrote:

Dear Michael, others,

Thank you for your quick response back on the 12th of March, I appreciate it. First and foremost I hope you’re all doing well under the current circumstances.

I stumbled upon something what seems like a discrepancy between the mappings returned by the API calling "/ontologies/:ontology/classes/:cls/mappings” and "/mappings?ontologies=ONT1,ONT2”. When I try to get mappings between a pair of ontologies involving SNOMED CT, I get different results.

For example, I want to check if this mappings exists in BioPortal: http://www.orpha.net/ORDO/Orphanet_3389<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389&data=02%7C01%7Cp.vandamme%40amsterdamumc.nl%7C96fd498830434d7bf44808d7dda46413%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C0%7C637221570442163072&sdata=CE7PbjVrayH7pjA2uwVe2AsX5%2BkL%2FYz%2Fc6pn5g8ovpQ%3D&reserved=0> = http://purl.bioontology.org/ontology/SNOMEDCT/56717001<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F56717001&data=02%7C01%7Cp.vandamme%40amsterdamumc.nl%7C96fd498830434d7bf44808d7dda46413%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C1%7C637221570442173065&sdata=UGaosLiUz9ZaicxBF1EyqtcdB8tYBtOtmAoFsI9oQIw%3D&reserved=0>. I can use the API calling
http://data.bioontology.org/ontologies/ORDO/classes/http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389/mappings<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fontologies%2FORDO%2Fclasses%2Fhttp%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389%2Fmappings&data=02%7C01%7Cp.vandamme%40amsterdamumc.nl%7C96fd498830434d7bf44808d7dda46413%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C1%7C637221570442183061&sdata=HjpAr3UKN9lvgUGbFC3qCU0syLh922rDU0zrtJRRxeM%3D&reserved=0>
or http://data.bioontology.org/mappings?ontologies=ORDO,SNOMEDCT<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fmappings%3Fontologies%3DORDO%2CSNOMEDCT&data=02%7C01%7Cp.vandamme%40amsterdamumc.nl%7C96fd498830434d7bf44808d7dda46413%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C1%7C637221570442183061&sdata=3W7%2F1o9DTZNtj5X2DSE0mRRsQs60%2F5eUnowuQek10so%3D&reserved=0> and check if the mapping exists. However, when I compare the returned set from the API calls above with https://bioportal.bioontology.org/ontologies/ORDO?p=classes&conceptid=http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389#mappings<https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FORDO%3Fp%3Dclasses%26conceptid%3Dhttp%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389%23mappings&data=02%7C01%7Cp.vandamme%40amsterdamumc.nl%7C96fd498830434d7bf44808d7dda46413%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C1%7C637221570442193057&sdata=lqb4RXc0BwVKbiSIS%2Bn4d7APAQAVtmRiPM%2Bvf6Ng8bQ%3D&reserved=0> I noticed the following:

  *   The mapping exists according to the class mappings on the webpage, referring to URI http://purl.bioontology.org/ontology/SNOMEDCT/56717001<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F56717001&data=02%7C01%7Cp.vandamme%40amsterdamumc.nl%7C96fd498830434d7bf44808d7dda46413%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C1%7C637221570442193057&sdata=jv%2BxNjoV68ur%2B68An1meF0LjsLcyzZEaXV4V5isAy%2BQ%3D&reserved=0> and SNOMEDCT.


Yes, I confirm that I see the same.



  *   The mapping exists according to http://data.bioontology.org/ontologies/ORDO/classes/http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389/mappings<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fontologies%2FORDO%2Fclasses%2Fhttp%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389%2Fmappings&data=02%7C01%7Cp.vandamme%40amsterdamumc.nl%7C96fd498830434d7bf44808d7dda46413%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C1%7C637221570442203056&sdata=hsftEAxXI%2FoEX7ZestFYO0jIcTpgmdqp9fx5LwJilRM%3D&reserved=0>, however, using different URI (http://snomed.info/id/56717001<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsnomed.info%2Fid%2F56717001&data=02%7C01%7Cp.vandamme%40amsterdamumc.nl%7C96fd498830434d7bf44808d7dda46413%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C1%7C637221570442213046&sdata=%2FfJZBnDeafRZ060%2FTpA%2BRm%2BIXJE4FFC%2F7q8%2F4vM%2BuLU%3D&reserved=0>) and referring to ontology SNO_COPY which is not accessible.


I don’t see the same here. I issued the REST call that you list above, and the mapping between the Tuberculosis terms in ORDO and SNOMEDCT does exist in the result set. Here’s a screen shot showing the LOOM mapping:


[cid:CAB488B4-906C-417D-8302-942F2DB18543 at stanford.edu]


I also see the other mapping you referred to, i.e., the LOOM mapping between the Tuberculosis terms in ORDO and SNO_COPY:


[cid:7854C9AF-8DD7-4B34-A1D3-FB605FC4FE02 at stanford.edu]


With regard to this latter case, I see two issues:

1). There's a known issue with the BioPortal REST API where the mappings endpoint returns results that include terms from private ontologies (documented here: https://github.com/ncbo/ontologies_api/issues/52). SNO_COPY is a private ontology, which is why it’s not accessible to you.
2). There appears to be a duplicate of the same LOOM mapping from Tuberculosis in ORDO to Tuberculosis in SNO_COPY. It’s not immediately clear to me why the duplicate exists. I’ve entered a new issue in our tracker: https://github.com/ncbo/ontologies_api/issues/67.



  *   The mappings doesn’t exist according to http://data.bioontology.org/mappings?ontologies=ORDO,SNOMEDCT<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fmappings%3Fontologies%3DORDO%2CSNOMEDCT&data=02%7C01%7Cp.vandamme%40amsterdamumc.nl%7C96fd498830434d7bf44808d7dda46413%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C1%7C637221570442213046&sdata=R6L3sQQcnVR8dEpAUf33of7tu1S2Hyn2dCBOCFFVVsM%3D&reserved=0>.


Yes, I confirm that I see the same. There’s a known issue with the BioPortal REST API where occasional irregularities exist between result sets from the /mappings and /classes/:cls/mappings endpoints. That issue is documented in our GitHub repository, and I’ve added your observations just now: https://github.com/ncbo/ontologies_api/issues/50#issuecomment-620784355.



I decided to only use mappings from http://data.bioontology.org/mappings?ontologies=ORDO,SNOMEDCT<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fmappings%3Fontologies%3DORDO%2CSNOMEDCT&data=02%7C01%7Cp.vandamme%40amsterdamumc.nl%7C96fd498830434d7bf44808d7dda46413%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C1%7C637221570442223042&sdata=oDFTyhR44021QpzPUvYoViVzb6MOYvtqbmVD4YZ9Z%2Fs%3D&reserved=0>, but that still makes me wonder why the webpage shows SNOMED CT mappings that are not returned by the API in the same way (point 1 vs. point 2). Am I missing something? I checked http://data.bioontology.org/mappings?ontologies=ORDO,SNO_COPY<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fmappings%3Fontologies%3DORDO%2CSNO_COPY&data=02%7C01%7Cp.vandamme%40amsterdamumc.nl%7C96fd498830434d7bf44808d7dda46413%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C1%7C637221570442233040&sdata=DC6ZnwEewmNtyEwVnyNDuQsOhGw8bRq5vg6QxwDqZZA%3D&reserved=0>, which is returning an empty set.


No, you’re not missing something. As I mentioned above, you’ve run into a known issue with the API.

Hope these explanations were helpful.

Kind regards,
Jennifer

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