add compound tissue term 2

[zhilianghu]

Preferred term label: Uterine endometrium caruncular

Synonyms

Definition (free text, please give PubMed ID) Caruncules on inner lining layer of the uterus.

Parent term (use https://www.ebi.ac.uk/ols/ontologies/uberon) Uterine

Your nano-attribution (ORCID) ORCID: 0000-0002-6704-7538

[cmungall]

Could we have someone with comparative placental anatomy look at this? I think this refers to non human structures. There are terminologically similar uterine caruncles in human (barely in scope, we have precedent with Nevis) but I think these are distinct.

Thanks!! On Fri, Sep 8, 2023 at 1:26 PM Zhiliang Hu @.***> wrote:

Preferred term label: Uterine endometrium caruncular

Synonyms

Definition (free text, please give PubMed ID) Caruncules on inner lining layer of the uterus.

Parent term (use https://www.ebi.ac.uk/ols/ontologies/uberon https://www.ebi.ac.uk/ols/ontologies/uberon) Uterine

Your nano-attribution (ORCID) ORCID: 0000-0002-6704-7538

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[zhilianghu]

Thank you Chris for quickly picking it up.

Uterine endometrium, or Uterine endometrium caruncular, can be viewed as “compound concept” (each part is a stand-alone tissue concept).

I feel compelled to share some thoughts on how “compound tissue/organ” concepts could be better covered while not to be too granule (applications often seen in functional annotations of genomes using nextgen sequencing, eg. SRA data, where all sorts of sampling variations are seen, and need be better represented with a formal ontology like Uberon)?

Following a model where we used “modifiers” to describe “trait variants” at experiment level when annotate QTL/association data in QTLdb (https://doi.org/10.1093/database/baad024), I introduced “sampling conditions” as modifiers to handle variations when I map tissue names to Uberon/ Brenda Tissue Ontology/ etc in my works on EpiDB (https://epidb.animalgenome.org/). In cases like “uterine endometrium” or “uterine endometrium caruncular”, the “modifier” is not life stage/ anatomy location/ organ parts but another tissue concept.

I understand an ontology cannot go too much into fine granularities, but besides providing a “text book” like resource how far it may extend to help out in research fields (where situations can be complex)? ... I better stop here.

Thank you for your time.

Zhiliang

From: Chris Mungall @.> Reply-To: obophenotype/uberon @.> Date: Fri, Sep 08, 2023 at 09:06 PM To: obophenotype/uberon @.> Cc: Zhiliang Hu @.>, Author @.***> Subject: Re: [obophenotype/uberon] add compound tissue term 2 (Issue #3064)

Could we have someone with comparative placental anatomy look at this? I think this refers to non human structures. There are terminologically similar uterine caruncles in human (barely in scope, we have precedent with Nevis) but I think these are distinct.

Thanks!! On Fri, Sep 8, 2023 at 1:26 PM Zhiliang Hu @.***> wrote:

Preferred term label: Uterine endometrium caruncular

Synonyms

Definition (free text, please give PubMed ID) Caruncules on inner lining layer of the uterus.

Parent term (use https://www.ebi.ac.uk/ols/ontologies/uberon https://www.ebi.ac.uk/ols/ontologies/uberon) Uterine

Your nano-attribution (ORCID) ORCID: 0000-0002-6704-7538

— Reply to this email directly, view it on GitHub https://github.com/obophenotype/uberon/issues/3064, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAMMOKLEUKPU2HKCYYNFIDXZN5P3ANCNFSM6AAAAAA4Q3T7ZI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

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