ResearchStudy.condition coding inconsistencies between dbGap, AnVIL and KidsFirst

[bwalsh]

We should use the same ontologies (or provide mappings).
While all three systems use ResearchStudy.condition to indicate the condition that is the focus of the study.
All three have a significant number of studies without a populated condition.
In addition, all three systems use different ontologies:

system:
ontology system: study_count

* 'kidsfirst': 
    * None: 21,
    * 'http://snomed.info/sct': 8
* 'dbgap':
    * None: 234,
    * 'https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm': 1597,
    * 'https://uts.nlm.nih.gov/metathesaurus.html': 1459,
    * 'urn:oid:2.16.840.1.113883.6.177': 1591    
* 'anvil':
    * None: 358,
    * 'http://purl.obolibrary.org/obo/doid.owl': 35

[linikujp]

Hi Brian, the FHIR ResearchStudy condition and focus are two different things.
Some studies do not have a condition, because the study does not focus on conditions, rather than normal sample as a control or reference. We have explored this when looking at the NCPI data catalog.

Thanks,
Asiyah

[bwalsh]

Hi Brian, the FHIR ResearchStudy condition and focus are two different things. Some studies do not have a condition, because the study does not focus on conditions, rather than normal sample as a control or reference. We have explored this when looking at the NCPI data catalog.

Thanks, Asiyah

@linikujp

Hi Asiyah,

Agreed that condition and focus are two different things - that may explain at least some of the studies without a Condition.

However, where there is a condition, I'm concerned that we have 5 different ontology systems.

• What guidance would we provide to researchers searching by condition?
• What might we do to reduce the number of ontologies used or simplify mapping between them?

[linikujp]

Hi Brian,
Can you list the 5 different ontology systems? I have done some work of mapping DO-MONDO-MeSH for NCPI data catalog. which is based on the dbGaP FHIR server. I also have some experience with ontology harmonization or alignment, and I am working with DO and MONDO to resolve the inconsistencies I see from NCPI use case. If you list the 5 ontologies out, we may make a case for aligning all these 5 ontologies for the NCPI community.
Thanks,
Asiyah

[bwalsh]

If you list the 5 ontologies out, we may make a case for aligning all these 5 ontologies for the NCPI community.

From above ...
Thanks!
-b

• 'kidsfirst':
  * None: 21,
  * 'http://snomed.info/sct': 8
• 'dbgap':
  * None: 234,
  * 'https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm': 1597,
  * 'https://uts.nlm.nih.gov/metathesaurus.html': 1459,
  * 'urn:oid:2.16.840.1.113883.6.177': 1591
• 'anvil':
  * None: 358,
  * 'http://purl.obolibrary.org/obo/doid.owl': 35

[linikujp]

Do you know what this is for: urn:oid:2.16.840.1.113883.6.177

…

On Thu, Dec 2, 2021, 18:31 Brian ***@***.***> wrote: If you list the 5 ontologies out, we may make a case for aligning all these 5 ontologies for the NCPI community. From above ... Thanks! -b - 'kidsfirst': * None: 21, * 'http://snomed.info/sct': 8 - 'dbgap': * None: 234, * ' https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm': 1597, * 'https://uts.nlm.nih.gov/metathesaurus.html': 1459, * 'urn:oid:2.16.840.1.113883.6.177': 1591 - 'anvil': * None: 358, * 'http://purl.obolibrary.org/obo/doid.owl': 35 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#44 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACCPEPIDBFY5R4BEOXZM2DLUO76UFANCNFSM5JFVHB6A> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[bwalsh]

I'm traveling now, and will be out of office next week. Will follow up then. As far as I know: https://www.hl7.org/documentcenter/public/standards/vocabulary/vocabulary_tables/infrastructure/vocabulary/voc_ExternalSystems.html

…

On Thu, Dec 2, 2021, 4:21 PM Asiyah Yu Lin ***@***.***> wrote: Do you know what this is for: urn:oid:2.16.840.1.113883.6.177 On Thu, Dec 2, 2021, 18:31 Brian ***@***.***> wrote: > If you list the 5 ontologies out, we may make a case for aligning all > these 5 ontologies for the NCPI community. > > From above ... > Thanks! > -b > > > - 'kidsfirst': > * None: 21, > * 'http://snomed.info/sct': 8 > - 'dbgap': > * None: 234, > * ' > https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm': > 1597, > * 'https://uts.nlm.nih.gov/metathesaurus.html': 1459, > * 'urn:oid:2.16.840.1.113883.6.177': 1591 > - 'anvil': > * None: 358, > * 'http://purl.obolibrary.org/obo/doid.owl': 35 > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > < #44 (comment) >, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/ACCPEPIDBFY5R4BEOXZM2DLUO76UFANCNFSM5JFVHB6A > > . > Triage notifications on the go with GitHub Mobile for iOS > < https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 > > or Android > < https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub >. > > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#44 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAALVQGSNB2ZVQYU4L5CPBTUPAEO5ANCNFSM5JFVHB6A> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[RobertJCarroll]

It looks like that urn is mesh again.

Based on our prior conversations, it sounded like "Given we are using these ResearchStudy objects as a way to do information retrieval, MeSH is a good target". The field is a codeable concept, so we can have a custom free text and multiple ancillary concepts included. IE, if I'd like to flag with SNOMED concept, great, but I should also include the MeSH term that's most relevant.