Terms to add to imports

[lschriml]

NCBI taxonomy

Microsporum canis Microsporum gypseum Fonsecaea pedrosoi Fonsecaea compacta Cladophialophora carrionii Phialophora verrucosa Piedraia hurtae Malassezia furfur Hortaea werneckii Trichosporon beigelii

Aspergillus fumigatus Curvularia hawaiiensis Cladosporium cladosporoides

Black Creek Canal orthohantavirus Echovirus Onyong-nyong virus

UBERON: hand foot fingers

[lschriml]

SO terms updated:

• adding back terms:

loss_of_function_variant

maternal_uniparental_disomy SO:0001745 paternal_uniparental_disomy SO:0001746 maternally_imprinted SO:0000135

chromosomal_translocation. SO:1000044 paternal_variant SO:0001776 maternal_variant SO:0001775 gremlin_variant SO:0001778 somatic_variant SO:0001777 chromosomal_deletion SO:1000029 chromosomal_duplication SO:1000037 chromsomal_translocation SO:0000453 chromosomal_inversion SO:1000030 maternally_imprinted SO:0000135 chromosome_variation SO:0000240 chromosome_structure_variation SO:1000183 interchromosomal_translocation SO:0002060

[lschriml]

Looking at UBERON:

terms needed for DO: UBERON label hand manus foot pes finger manual digit thumb manual digit 1 cerebrum telencephalon

-- updated labels in uberon_terms.txt

Is there a programmatic way to make sure these labels stay in place when uberon import.owl file is created ?

[beckyjackson]

Are these different labels than the source ontology?

[lschriml]

Yes, They synonyms of Uberon terms.

Sent from my iPhone

On May 18, 2021, at 5:07 PM, Becky Jackson @.***> wrote:

 Are these different labels than the source ontology?

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[beckyjackson]

There is no method to change the labels of imported terms right now. ROBOT doesn't really have an easy way to do this... We have new python tools for working with ontologies that could accomplish this, but we'd have to rework the import workflow to use them.

Aside from that, I think typically it isn't the best idea to relabel imported terms. That's how we've ended up with multiple labels on terms from import modules, which has caused issues with ROBOT reports. Why would we need to relabel these terms if these are already synonyms?

[lschriml]

I agree Becky, it isn't the best idea to relabel. However, for these few terms, where the uberon label is non human and the synonym is a human anatomy term, I think we need to relabel. I asked Chris Mungall about this years ago and he said it was OK in this type of case to relabel. The terms: relabel. uberon term cerebrum telencephalon hand manus foot pes finger manual digit thumb digit 1

No one querying DO would think to query by one of these uberon non-human terms, when searching for one of the 'relabel' terms.

Cheers, Lynn

On Wed, May 19, 2021 at 12:45 AM Becky Jackson @.***> wrote:

There is no method to change the labels of imported terms right now. ROBOT doesn't really have an easy way to do this... We have new python tools for working with ontologies that could accomplish this, but we'd have to rework the import workflow to use them.

Aside from that, I think typically it isn't the best idea to relabel imported terms. That's how we've ended up with multiple labels on terms from import modules, which has caused issues with ROBOT reports. Why would we need to relabel these terms if these are already synonyms?

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-- Lynn M. Schriml, Ph.D. Associate Professor

Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 @.***

[lschriml]

@beckyjackson -- Checking with you to see if I add the new taxonomy terms ? or do you prefer to add them ?

Cheers, Lynn

[beckyjackson]

Hi Lynn - please feel free to add them, but they will not have the updated labels because our workflow doesn't have a way to do this right now. I will need to rework the import workflow to allow label updates.

[allenbaron]

Notes about TAXONOMY terms to be added:

1. "Microsporum gypseum" is not available in NCBItaxon (a search of NCBI's taxonomy directly returns Nannizzia gypsea).

2. NCBItaxon has both "Echovirus" (NCBITaxon:33758) and "Human echovirus" (NCBITaxon:1569923). Both are currently classified as siblings in NCBItaxon below "unclassified Enterovirus".

   • There are other (human) echoviruses listed as well.
   • Is adding "Echovirus" sufficient?

3. Name discrepancies:

   1. Cladosporium cladosporoides is "Cladosporium cf. cladosporoides" in NCBItaxon.
   2. Piedraia hurtae is "Piedraia hortae" in NCBItaxon.

[allenbaron]

UBERON updates:

• Added "finger" (manual digit; UBERON:0002389)
• All UBERON terms listed above have now been added.

Next step convert labels to human-specific synonyms.

[allenbaron]

I did an expanded check while working on #1052 to make sure all NCBITaxon terms were in the newest import and four previously added terms in the ncbitaxon_terms.txt file are no longer in the import. They were also missing from the source file (latest release: 2022-06-28).

The four terms are:

id	label
NCBITaxon:12461	Hepatitis E virus
NCBITaxon:1535326	Candida <Debaryomycetaceae>
NCBITaxon:27317	Galactomyces geotrichum
NCBITaxon:489714	Microsporum gypseum

---

The last time ncbitaxon_import.owl was updated was 2021-03-23 (commit 700d7a10). The corresponding release for NBITaxon was v2021-02-15.

I checked that file and only NCBITaxon:12461 & NCBITaxon:1535326 were present.

I'm working to track down what happened to these taxa and what there replacements are, if any. These changes will probably necessitate updating axioms in DO.

[lschriml]

Great !! Thank you Allen !!

On Wednesday, July 13, 2022, J. Allen Baron @.***> wrote:

I did an expanded check while working on #1052 https://github.com/DiseaseOntology/HumanDiseaseOntology/pull/1052 to make sure all NCBITaxon terms were in the newest import and four previously added terms in the ncbitaxon_terms.txt file are no longer in the import. They were also missing from the source file (latest release: 2022-06-28 https://github.com/obophenotype/ncbitaxon/releases/tag/v2022-06-28).

The four terms are: id label NCBITaxon:12461 Hepatitis E virus NCBITaxon:1535326 Candida NCBITaxon:27317 Galactomyces geotrichum NCBITaxon:489714 Microsporum gypseum

The last time ncbitaxon_import.owl was updated was 2021-03-23 (commit 700d7a1 https://github.com/DiseaseOntology/HumanDiseaseOntology/commit/700d7a102c9feb7f9316806a27d4ed2b40a55b2c). The corresponding release for NBITaxon was v2021-02-15 https://github.com/obophenotype/ncbitaxon/releases/tag/v2021-02-15.

I checked that file and only NCBITaxon:12461 & NCBITaxon:1535326 were present.

I'm working to track down what happened to these taxa and what there replacements are, if any. These changes will probably necessitate updating axioms in DO.

— Reply to this email directly, view it on GitHub https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/946#issuecomment-1183717566, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBB4DL2YWAFYUZHB5K3EI3VT43RFANCNFSM45A5TVHQ . You are receiving this because you were assigned.Message ID: @.***>

-- Lynn M. Schriml, Ph.D. Associate Professor

Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 @.***