Details about Term properties

[asoket]

Hello, Looking for detail documentation on NCIt Term elements (properties) used in "ncit.obo". There are total 23 elements in the "ncit.obo" file used in different combinations. These elements are namely: "id", "name", "def", "subset", "synonym", "is_a", "relationship", "property_value", "xref", "is_obsolete", "comment", "data-version", "disjoint_from", "domain", "format-version", "intersection_of", "is_transitive", "ontology", "range", "remark", "subsetdef", "[Term]", "[Typedef]". Looking for documentation similar to the Gene Ontology file "go.obo" as available at http://geneontology.org/docs/GO-term-elements.

[balhoff]

@asoket it sounds like you are looking for documentation on the OBO format itself? If so, is this useful? https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_4.html

[asoket]

@balhoff It is useful indeed. Thank you so much.

[asoket]

@balhoff I have a few more questions.

1. In the ncit.obo file, I find NCIT:Pnnn and NCIT:Annn codes are used in the "property_value" element/property of many NCIT Terms. However I do not find any Term in ncit.obo with any of these ids. However, at OLS Ontology search at https://www.ebi.ac.uk/ols/search?q=NCIT_P98&ontology=ncit I can find NCIT:P98 and other "P" & "A" Terms with only "name" and "def". Is there any location where I can find the complete ontology on all Pnnn & Annn? Or can I download all terms associated with "P" and "A".
2. Is there any documentation that will help me understand the functional aspect of elements/properties like "property_value", "relationship" etc. beyond what is explained in https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_4.html?
3. I am trying to build an oncology knowledge graph from the ncit that can be easily accessed by an oncologist at the point-of-care integrated with the hospital EHR.

[asoket]

@balhoff some more points:

1. In "id: NCIT:C10000" of ncit.obo we have "property_value: NCIT:P310 "Obsolete_Concept" xsd:string". Does this mean that this is equivalent to "is_obsolete: true"?
2. In "id: NCIT:C77696", we have "property_value: NCIT:P98 "Wed Mar 21 17:54:09 EDT 2012 - Obsolete term, delisted from UNII" xsd:string". Is it equivalent to "is_obsolete: true" for this term?

[balhoff]

Hi @asoket,

In the ncit.obo file, I find NCIT:Pnnn and NCIT:Annn codes are used in the "property_value" element/property of many NCIT Terms. However I do not find any Term in ncit.obo with any of these ids. However, at OLS Ontology search at https://www.ebi.ac.uk/ols/search?q=NCIT_P98&ontology=ncit I can find NCIT:P98 and other "P" & "A" Terms with only "name" and "def". Is there any location where I can find the complete ontology on all Pnnn & Annn? Or can I download all terms associated with "P" and "A".

This seems like a problem with the OBO format file. These terms (e.g., NCIT:P98) are properly defined in the OWL syntax version, which is what OLS is loading:

 <!-- http://purl.obolibrary.org/obo/NCIT_P98 -->

    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/NCIT_P98">
        <obo:IAO_0000115>A property representing notations made by NCI vocabulary curators. They are intended to provide supplemental, unstructured information to the user or additional insight about the concept.</obo:IAO_0000115>
        <obo:NCIT_NHC0>P98</obo:NCIT_NHC0>
        <obo:NCIT_P106>Conceptual Entity</obo:NCIT_P106>
        <obo:NCIT_P107>DesignNote</obo:NCIT_P107>
        <obo:NCIT_P108>DesignNote</obo:NCIT_P108>
        <oboInOwl:hasExactSynonym>DesignNote</oboInOwl:hasExactSynonym>
        <rdfs:label>DesignNote</rdfs:label>
        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
    </owl:AnnotationProperty>

Thanks for pointing this out!

Is there any documentation that will help me understand the functional aspect of elements/properties like "property_value", "relationship" etc. beyond what is explained in https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_4.html?

The OBO format documentation is primarily written in terms of how it maps to the OWL language, which is much more formally specified. A good place to start with OWL is here: https://www.w3.org/TR/owl2-primer/ If you are writing software to work with ontologies, I personally recommend using one of the OWL syntaxes rather than OBO, and using a standard RDF or OWL parser to do the parsing.

I am trying to build an oncology knowledge graph from the ncit that can be easily accessed by an oncologist at the point-of-care integrated with the hospital EHR.

As part of this project I created a simplified graph from NCIT using OWL reasoning; you might be interested: https://github.com/NCI-Thesaurus/thesaurus-obo-edition/wiki/NCIt-graph-queries

In "id: NCIT:C10000" of ncit.obo we have "property_value: NCIT:P310 "Obsolete_Concept" xsd:string". Does this mean that this is equivalent to "is_obsolete: true"?

I think so, but NCIT provides some other fine-grained statuses like "Retired_Concept"; I not sure exactly what the difference is.

In "id: NCIT:C77696", we have "property_value: NCIT:P98 "Wed Mar 21 17:54:09 EDT 2012 - Obsolete term, delisted from UNII" xsd:string". Is it equivalent to "is_obsolete: true" for this term?

I wouldn't say it's equivalent; it just provides some extra information about the obsoletion.

[asoket]

Thank you so much for your help. -- Kind Regards & Thank You in Advance. Asoke K Talukder, Ph.D

…

On Tue, Jul 13, 2021 at 11:42 PM Jim Balhoff ***@***.***> wrote: Hi @asoket <https://github.com/asoket>, In the ncit.obo file, I find NCIT:Pnnn and NCIT:Annn codes are used in the "property_value" element/property of many NCIT Terms. However I do not find any Term in ncit.obo with any of these ids. However, at OLS Ontology search at https://www.ebi.ac.uk/ols/search?q=NCIT_P98&ontology=ncit I can find NCIT:P98 and other "P" & "A" Terms with only "name" and "def". Is there any location where I can find the complete ontology on all Pnnn & Annn? Or can I download all terms associated with "P" and "A". This seems like a problem with the OBO format file. These terms (e.g., NCIT:P98) are properly defined in the OWL syntax version, which is what OLS is loading: <!-- http://purl.obolibrary.org/obo/NCIT_P98 --> <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/NCIT_P98"> <obo:IAO_0000115>A property representing notations made by NCI vocabulary curators. They are intended to provide supplemental, unstructured information to the user or additional insight about the concept.</obo:IAO_0000115> <obo:NCIT_NHC0>P98</obo:NCIT_NHC0> <obo:NCIT_P106>Conceptual Entity</obo:NCIT_P106> <obo:NCIT_P107>DesignNote</obo:NCIT_P107> <obo:NCIT_P108>DesignNote</obo:NCIT_P108> <oboInOwl:hasExactSynonym>DesignNote</oboInOwl:hasExactSynonym> <rdfs:label>DesignNote</rdfs:label> <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/> </owl:AnnotationProperty> Thanks for pointing this out! Is there any documentation that will help me understand the functional aspect of elements/properties like "property_value", "relationship" etc. beyond what is explained in https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_4.html? The OBO format documentation is primarily written in terms of how it maps to the OWL language, which is much more formally specified. A good place to start with OWL is here: https://www.w3.org/TR/owl2-primer/ If you are writing software to work with ontologies, I personally recommend using one of the OWL syntaxes rather than OBO, and using a standard RDF or OWL parser to do the parsing. I am trying to build an oncology knowledge graph from the ncit that can be easily accessed by an oncologist at the point-of-care integrated with the hospital EHR. As part of this project I created a simplified graph from NCIT using OWL reasoning; you might be interested: https://github.com/NCI-Thesaurus/thesaurus-obo-edition/wiki/NCIt-graph-queries In "id: NCIT:C10000" of ncit.obo we have "property_value: NCIT:P310 "Obsolete_Concept" xsd:string". Does this mean that this is equivalent to "is_obsolete: true"? I think so, but NCIT provides some other fine-grained statuses like "Retired_Concept"; I not sure exactly what the difference is. In "id: NCIT:C77696", we have "property_value: NCIT:P98 "Wed Mar 21 17:54:09 EDT 2012 - Obsolete term, delisted from UNII" xsd:string". Is it equivalent to "is_obsolete: true" for this term? I wouldn't say it's equivalent; it just provides some extra information about the obsoletion. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#72 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AG77GP6JIJPNZUYG4RRQ2X3TXR6ZLANCNFSM4757KGDA> .