opmi / opmi

OPMI: Ontology of Precision Medicine and Investigation

OPMI-ontology

OPMI: Ontology of Precision Medicine and Investigation

This GitHub website is the home page of OPMI.

OPMI is an application ontology to support precision medicine and related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles. OPMI reuses, aligns, and integrates related terms from existing ontologies in the OBO ontology liborary.

OPMI was first developed by extracting general precision medicine related terms from the Ontology of Respiratory Disease Investigation (ORDI). Primarily developed by Drs. Hong Yu, Jie Zheng, and Oliver He, ORDI is an application ontology aimed to represent ontology terms related to respiratory diseases and related investigations. Dr. Hong Yu is a respiratory disease clinician and professor. ORDI was developed to represent the entities and relations related to clinical phenotypes, lab testing, and working environmental conditions, social economic situations, etc. The ORDI work with its use case study was presented in the Biocuration-2018 conference held at Shanghai, China.

OPMI is now supported by the new NIH/NIDDK-supported Kidney Precision Medicine Project (KPMP, http://kpmp.org). With >20 universities/institutes involved, KPMP aims to study a large number of human subjects with the acute kidney injury (AKI) and chronic kidney disease (CKD). As requested by the KPMP consortium, OPMI aims to represent and standardize the entities associated with precision medicine, including all the data/metadata types, investigation processes, and analysis in various aspects of clinical, pathological, and molecular studies to be conducted in KPMP. Example KPMP data types include clinical electronical health record types, pathological image data types, and various Omics data types.

OPMI has now been approved to be an OBO Foundry library ontology: http://obofoundry.org/ontology/opmi.html.

Collaborations are welcome. A very active collaboration OPMI has is the the collaboration with clinicaltrials.gov and many collaborators to develop clinical trial-specific terms with the aim to standardize and integrate clinical trial data. See more details in the meeting notes: https://docs.google.com/document/d/1VnmFhqFwfH3qcShiZUTO9ALF-3JKCs2oa3MQ2LotH6U/edit.

Download

Use the following URI to download this ontology

• http://purl.obolibrary.org/obo/opmi.owl

Note that the source ontology is an OWL file.

Deposition and Browsing

• Default browsing in Ontobee: http://www.ontobee.org/ontology/OPMI
• Browsing in NCBO BioPortal: https://bioportal.bioontology.org/ontologies/OPMI

OPMI in OBO Foundry:

http://obofoundry.org/ontology/opmi.html.

Publication

• He Y, Ong E, Schaub J, Dowd F, O’Toole JF, Siapos A, Reich C, Seager S, Wan L, Yu H, Zheng J, Stoeckert C, Yang X, Yang S, Steck B, Park C, Barisoni L, Kretzler M, Himmelfarb J, Iyengar R, Mooney SD, for the Kidney Precision Medicine Project Consortium. OPMI: the Ontology of Precision Medicine and Investigation and its support for clinical data and metadata representation and analysis. The 10th International Conference on Biomedical Ontology (ICBO-2019), July 30 - August 2, 2019, Buffalo, NY, USA. 10-page full length article.

opmi's Issues

Wrong use of oboInOwl namespace

http://www.geneontology.org/formats/oboInOWL#hasAlternativeId
http://www.geneontology.org/formats/oboInOWL#hasBroadSynonym
http://www.geneontology.org/formats/oboInOWL#hasExactSynonym
http://www.geneontology.org/formats/oboInOWL#hasNarrowSynonym
http://www.geneontology.org/formats/oboInOWL#hasRelatedSynonym
http://www.geneontology.org/formats/oboInOWL#xref

Should be:

http://www.geneontology.org/formats/oboInOwl#hasExactSynonym

(note capitalisation).

Note that:
http://www.geneontology.org/formats/oboInOWL#xref

Is wrong in general. Should be:
http://www.geneontology.org/formats/oboInOwl#hasDbXref

Context: Our grand OBO wide ID normalisation effort.
https://github.com/orgs/OBOFoundry/projects/5

specimen barcode

Hi,
I was thinking of potentially using OPMI's 'specimen barcode' in the Influenza Ontology, using it to replace FLU's version of 'specimen barcode' (as that term is not specific to influenza). But I wanted to ensure consistency first.

I noticed that the OPMI superclass 'barcode' is classified as a IAO:CRID. It appears to me that this isn't consistent with IAO's stance on CRIDs. According to an editor note on 'CRID', Universal Product Code barcodes are not CRIDs, as they are not centrally registered. In that case not every barcode is a CRID.

So I am not sure whether 'specimen barcodes' are CRIDs. Does a specimen barcode always have information about the CRID registry to which it belongs?

Currently, the FLU version of 'specimen barcode' is classified as a 'specimen ID', a term from OBIB. Specimen ID is a subclass of IAO:identifier.

Additional Logs/Comments to Dec 8 2018 commit.

This issue is submitted to add additional logs and comments to the commit 3070cd0 submitted by @yongqunh

Updated OPMI from Vision Release: 1.0.21 to 1.0.23. Changes are as follows:

1. Edited OBI_imports_input.txt Ontofox input.
   Changed OBI_0000075 commented label.
   Added OBI_0000066.
2. Updated OBI_imports.owl following Ontofox.
3. Edited opmi.owl to import OAE_imports.owl.
4. Edited opmi.owl terms:
   Changed OPMI_0000001 from "less than 8th grade completion" to "precision medicine process".
   The original "less than 8th grade completion" now has new IRI OPMI_0000017.
   Changed OPMI_0000002 from "less than 12th grade completion" to "precision medicine investigation"
   The original "less than 12th grade completion" now has new IRI OPMI_0000020
5. Updated opmi-merged.owl.

'role in human social processes' (OMRSE:00000024) has been deprecated and replaced

In the future we plan on reaching out to developers of ontologies that import our classes to get their input prior to making such changes, but we have replaced this class with another one with the same label: 'role in human social processes' (OMRSE:00002072). The only change to the class was to the subClassOf axiom, which we changed from "inheres-in only human or organization" to "inhere-in only 'material entity'."

status

The term 'status' is created in OPMI under the realizable entity (BFO) without a definition. This is a very important term. Definition and rational of status as a realizable entity is needed.

Number of hospitalizations

Need a new term 'number of hospitalizations', which indicates the number of hospitalizations of a patient in a hospital.

note that this term is required in Chinese medical record standardization.

How to define clinical trial phases and its relation with different clinical trials

Some discussion by Leon Li, Asiyah Lin, Oliver He:
What is a clinical trial phase? Is it a process, or process quality? If it is process quality, it should be a BFO continuant or occurrant? In PATO, process quality is a subclass of quality, which is listed as a continuant. However, the process quality is more like a BFO occurrant or process profile. This is an issue. Asiyah has submitted a request to BFO discuss.

Wrong use of IRIs

Hey! In our great OBO wide effort to fix our PURLs, I noticed the following wrong ones being used in UO:

• rdfs:seeAlso (used as an IRI!! not shortform)

New Term Request

As part of conversation regarding CIDO, I would ask the following terms be added to OPMI. If these would be better provided
Human Cohort (Defined as a collection of humans that is selected for common characteristics for some research study)
Human Cohort Age (Defined as a set of ages such that the age of any member of a human cohort is included in this set)
Human Cohort Biological Sex (Defined as a set of Biological Sex such that the age of any member of a human cohort is included in this set)

bad language tag: "Oliver He"@ualr.edu)

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OPMI_0000215"> ... <dc:creator xml:lang="ualr.edu)">Oliver He</dc:creator> <rdfs:label xml:lang="en">last four digits of social security number</rdfs:label> </owl:Class>

Welcome to OPMI ontology track issue site

Welcome to OPMI ontology track issue site!

OPMI donates terms to the Clinical Trial Ontology (CTO)

Dr. Oliver He and the OPMI team have been collaborating with Drs. Leon Li and Evan Bolton from NIH and Asiyah Lin from FDA to develop many clinical trial-specific terms to support the clinicaltrials.gov data standardization and integration, with an application to ingrate the clinical trial data with the data in PubChem. Later we also started to collaborate with Stephan Gebel and his group in Germany on this work. Stephan and his group had developed a Clinical Trial Ontology (CTO). After discussion, we decided to restructure the CTO based on the OBO Foundry principles and OBO ontology development methods. Oliver, Asiyah, and Leon actively worked with Stephan and his team to make the restructuring.
See the meeting notes on the collaborative work between OPMI and CTO project teams:
https://docs.google.com/document/d/1VnmFhqFwfH3qcShiZUTO9ALF-3JKCs2oa3MQ2LotH6U/edit

To make CTO more a reference ontology, in the meeting on May 15, 2020, Oliver proposed and agreed to donate a set of clinical trial-specific OPMI terms originally defined in OPMI to the new CTO ontology. See more information on the CTO tracker issue:
ClinicalTrialOntology/CTO#10

This is still an ongoing process. Any suggestions and comments are welcome.

Add obofoundry topic to repo metadata

The OBO Foundry has recently created a topics page at https://github.com/topics/obofoundry. It would be great if you could add the obofoundry topic to your repository, since it's currently listed as active in the OBO Foundry. If you're not sure how to do that, follow the instructions here. The main issue for this task is at OBOFoundry/OBOFoundry.github.io#1538 in case you want some more context or to join the larger discussion.