NTR: metacyclogenesis

[Achchuthan]

Can I request a new GO term entry for metacyclogenesis process please?

Accession: GO:xxxxxx Name: metacyclogenesis Ontology: biological_process Definition: The morphological, biochemical and genetic changes that induce the differentiation of non-pathogenic parasites into pathogenic metacyclic parasites in the Trypanosomatidae species. The pathogenic parasites are known as metacyclic trypomastigotes in Trypanosoma and metacyclic promastigotes in Leishmania. Taxonomic restriction: NCBITaxon:5654 ## Trypanosomatidae Source: PMID:12152483, PMID:21514274, PMID:2659372, PMID:29091711, PMID:29409544

Thanks & best wishes, Achchuthan

[cmungall]

We should include a link to the parasite life cycle term

On Wed, Oct 2, 2019 at 8:54 AM Achchuthan Shanmugasundram < notifications@github.com> wrote:

Can I request a new GO term entry for metacyclogenesis process please?

Accession: GO:xxxxxx Name: metacyclogenesis Ontology: biological_process Definition: The morphological, biochemical and genetic changes that induce the differentiation of non-pathogenic parasites into pathogenic metacyclic parasites in the Trypanosomatidae species. The pathogenic parasites are known as metacyclic trypomastigotes in Trypanosoma and metacyclic promastigotes in Leishmania. Taxonomic restriction: NCBITaxon:5654 ## Trypanosomatidae Source: PMID:12152483, PMID:21514274, PMID:2659372, PMID:29091711, PMID:29409544

Thanks & best wishes, Achchuthan

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[Achchuthan]

Thanks @cmungall. The metacyclic trypomastigote stage is OPL:0000149 and metacyclic promastigote stage is OPL:0000006

[Achchuthan]

Hi @pgaudet, I am wondering whether you had a chance to look at this request? Thanks a lot for your help. Best wishes, Achchuthan

[pgaudet]

Hi @cmungall I dont know how you want to add the references to the life stages. I tried 'occurs during' but I think we dont have the OPL ontology loaded.

Maybe @balhoff you know how to handle this ?

[pgaudet]

(sorry I just saw the ticket in the OPL ontology. I think I cannot add the xlinks for now).

[balhoff]

@pgaudet would you like to add an OPL import?

[pgaudet]

I think this is what @cmungall is asking, yes

[pgaudet]

New term:

id: GO:0140384 name: metacyclogenesis namespace: biological_process def: "The morphological, biochemical and genetic changes that induce the differentiation of non-pathogenic parasites into pathogenic metacyclic parasites in the Trypanosomatidae species. The pathogenic parasites are known as metacyclic trypomastigotes in Trypanosoma and metacyclic promastigotes in Leishmania." [PMID:12152483, PMID:21514274, PMID:2659372, PMID:29091711, PMID:29409544] is_a: GO:0044114 ! development of symbiont in host created_by: pg creation_date: 2019-11-20T13:25:55Z

[pgaudet]

PR for taxon constraint: https://github.com/geneontology/go-ontology/pull/18220

[pgaudet]

Still need to add

• [ ] links to the parasite life cycle term
• [x] taxon constraint (PR failed)

[Achchuthan]

Thanks a lot @pgaudet and @balhoff.

[pgaudet]

I dont know what to do next for this ticket.

[balhoff]

I added the import file. If you update you should be able to use the parasite terms now.

[pgaudet]

Hi @Achchuthan Can you please specific which stage is the end point of metacyclogenesis?

Thanks, Pascale

[Achchuthan]

Hi @pgaudet, There is no single end stage for metacyclogenesis across kinetoplastida parasites. The end stage of metacyclogenesis in Trypanosoma is metacyclic trypomastigote stage (OPL:0000149) and the end stage in Leishmania is metacyclic promastigote stage (OPL:0000006). Thanks, Achchuthan

[pgaudet]

@cmungall What do you recommend ? As far as I can tell the options are to either create two terms or to not include these terms.

Thanks, Pascale

[cmungall]

@Achchuthan @zhengj2007 - should OPL not include a generic grouping class "metacyclic stage" that groups the metacyclic stages in both taxa?

[zhengj2007]

Hi @cmungall OPL does not have term "metacyclic stage" and the term is not found in any other OBO Foundry ontologies. Do you mean OPL should add a new term "metacyclic stage"?

[cstoeckert]

OPL will work on adding a general metacyclic stage (which appears restricted to trypanosomatid parasites).

[pgaudet]

Added the term in olp-imports: https://github.com/geneontology/go-ontology/pull/18754

I can fix the LD once the imports have been regenerated.

[pgaudet]

@balhoff Can you please regenerate the OPL imports ?

[balhoff]

@pgaudet it doesn't look like OPL has made a new release yet.

[zhengj2007]

@pgaudet @balhoff We will make a new release soon.

[zhengj2007]

@pgaudet @balhoff The new release of OPL has been made. The required term is available, ‘Trypanosomatida metacyclic stage’ OPL_0000322.

The latest released OPL version IRI is: http://purl.obolibrary.org/obo/opl/2020-02-08/opl.owl

[pgaudet]

Added ends_with OPL:0000322 ! Trypanosomatida metacyclic stage.