New chemical terms

[CuzickA]

This ticket can be used to track chemical terms that will be added via spreadsheet/robot instead of manually in protege.

For https://github.com/PHI-base/curation/issues/152

Please create the following for PHI-ECO

• triflumizole
• bitertanol
• pyrifenox

(note to self, these chemicals have already been added to the updated anti-infective list)

Please create the following sets of terms for the three chemicals for PHIPO normal growth on ... resistance to ... sensitive to ...

Thanks @jseager7

[jseager7]

I'll use this initial set of chemicals to test the script that will automatically create PHIPO terms. I'm not going to focus on completely automating the PHI-ECO terms just yet, since we already have those partially automated.

If you want the PHI-ECO terms created soon, I'd recommend adding them to the term creation spreadsheet in the meantime.

[CuzickA]

Thanks, I've now added the PHI-ECO terms to the term creator sheet.

[jseager7]

@CuzickA I've added the chemical terms to PHIPO and PHI-ECO (see https://github.com/PHI-base/phi-eco/commit/937d8c4cd74ab3c1df7c35f8c0aa3d7b5710d8b1) and released both ontologies.

I've written a script to automate the creation of PHIPO and PHI-ECO terms. It works for me, but it will need to be tested on your machine.

[CuzickA]

@jseager7 In case you want to test the script I will need the following new terms for https://github.com/PHI-base/curation/issues/142

PHIPO normal growth on Prothioconazole sensitive to Prothioconazole resistance to Prothioconazole

PHI-ECO '+ Prothioconazole'

[CuzickA]

@jseager7 please create new terms need for https://github.com/PHI-base/curation/issues/192

PHIPO normal growth on fluopyram sensitive to fluopyram resistance to fluopyram

PHI-ECO '+ fluopyram'

(note to self: fluopyram is already included in the anti-infective list)

[CuzickA]

@jseager7 please create new terms need for https://github.com/PHI-base/curation/issues/199

PHIPO normal growth on kresoxim-methyl sensitive to kresoxim-methyl resistance to kresoxim-methyl

PHI-ECO '+ kresoxim-methyl'

(note to self: kresoxim-methyl is already included in the anti-infective list)

[CuzickA]

@jseager7 please create new terms need for PHI-base/curation#199

PHIPO normal growth on kresoxim-methyl sensitive to kresoxim-methyl resistance to kresoxim-methyl

PHI-ECO '+ kresoxim-methyl'

(note to self: kresoxim-methyl is already included in the anti-infective list)

Hi @jseager7, thank you for making these terms.

I was having some difficulty finding 'resistance to kresoxim-methyl' in PHI-Canto.

I can see it in PHIPO

When I search for the term id PHIPO:0001359 in PHI-Canto I see this 'resistance to' and the chemical name is blank.

Any ideas as to what has happened here?

The other terms are fine.

[CuzickA]

@jseager7 For https://github.com/PHI-base/curation/issues/193

Please add

PHIPO normal growth on isopyrazam sensitive to isopyrazam resistance to isopyrazam

PHI-ECO '+ isopyrazam'

(note to self: isopyrazam is already included in the anti-infective list)

[CuzickA]

Also for https://github.com/PHI-base/curation/issues/193

Please add

PHIPO normal growth on bixafen sensitive to bixafen resistance to bixafen

PHI-ECO '+ bixafen'

(note to self: bixafen is already included in the anti-infective list)

[CuzickA]

Also for https://github.com/PHI-base/curation/issues/193

Please add

PHIPO normal growth on carboxin

[jseager7]

When I search for the term id PHIPO:0001359 in PHI-Canto I see this 'resistance to' and the chemical name is blank.

@CuzickA Sorry about this, I've fixed the term name now. Somehow the chemical name had disappeared in the file before I committed it. I must've accidentally edited the OBO file somehow.

Please let me know if you need PHIPO reloaded today.

[CuzickA]

When I search for the term id PHIPO:0001359 in PHI-Canto I see this 'resistance to' and the chemical name is blank.

@CuzickA Sorry about this, I've fixed the term name now. Somehow the chemical name had disappeared in the file before I committed it. I must've accidentally edited the OBO file somehow.

Please let me know if you need PHIPO reloaded today.

Thanks for fixing this @jseager7. I can wait for the automated overnight load of PHIPO thanks.

[CuzickA]

Hi @jseager7 please add the following terms required for https://github.com/PHI-base/curation/issues/182

PHIPO normal growth on pyrimorph sensitive to pyrimorph resistance to pyrimorph

PHI-ECO '+ pyrimorph'

(note to self: pyrimorph is already included in the anti-infective list)

[CuzickA]

@jseager7 For https://github.com/PHI-base/curation/issues/146

Please add

PHIPO normal growth on tacrolimus sensitive to tacrolimus resistance to tacrolimus

exact synonym is 'FK506'

tacrolimus is already included in PHI-ECO

I have asked Jing to add it to the anti-infective list

[CuzickA]

Hi @jseager7 please add the following terms required for https://github.com/PHI-base/curation/issues/203

I don't see them as available terms in PHI-Canto so I assume we don't already have them in PHIPO and PHI-ECO. I don't have access to Protege at the moment, please could you double check so that we don't end up with duplicate terms.

PHIPO normal growth on fenpiclonil sensitive to fenpiclonil resistance to fenpiclonil

PHI-ECO '+ fenpiclonil'

(note to self: fenpiclonil is already included in the anti-infective list)

[jseager7]

I don't see them as available terms in PHI-Canto so I assume we don't already have them in PHIPO and PHI-ECO.

Fenpiclonil didn't exist in either ontology, so I've added the terms now.

[CuzickA]

Hi @jseager7, and another chemical to add please for https://github.com/PHI-base/curation/issues/201

Please could you double check we don't already have these

PHIPO normal growth on phenamacril sensitive to phenamacril resistance to phenamacril

PHI-ECO '+ phenamacril'

(note to self: phenamacril is already included in the anti-infective list)

[jseager7]

@CuzickA I've added terms for phenamacril.

[CuzickA]

Hi @jseager7 please add the following terms required for https://github.com/PHI-base/curation/issues/206

Please add 'SYP-Z048' as an exact synonym

PHIPO normal growth on pyrisoxazole sensitive to pyrisoxazole resistance to pyrisoxazole

PHI-ECO '+ pyrisoxazole'

(note to self: pyrisoxazole is already included in the anti-infective list)

[jseager7]

Please add 'SYP-Z048' as an exact synonym

@CuzickA Do you mean each term should have an exact synonym of the following format?

normal growth on pyrisoxazole → normal growth on SYP-Z048

[CuzickA]

Yes please, sorry for being unclear.

[jseager7]

No problem, it was clear enough, just making sure. :slightly_smiling_face:

[jseager7]

I've added the terms for pyrisoxazole and they all have SYP-Z048 in the exact synonym. For example:

AnnotationAssertion(oboInOwl:hasExactSynonym obo:PHIPO_0001389 "sensitive to SYP-Z048")

Same for PHI-ECO:

AnnotationAssertion(oboInOwl:hasExactSynonym obo:PECO_0005325 "+ SYP-Z048"^^xsd:string)

[CuzickA]

Hi @jseager7, please add chemical 'metconazole' for https://github.com/PHI-base/curation/issues/209

PHIPO normal growth on metconazole sensitive to metconazole resistance to metconazole

PHI-ECO '+ metconazole'

(note to self: metconazole is already included in the anti-infective list)

[jseager7]

I've added the phenotype terms and experimental condition for metconazole.

[CuzickA]

Hi @jseager7, please add chemical 'trifloxystrobin' for https://github.com/PHI-base/curation/issues/204

PHIPO normal growth on trifloxystrobin sensitive to trifloxystrobin resistance to trifloxystrobin

PHI-ECO '+ trifloxystrobin'

(note to self: trifloxystrobin is already included in the anti-infective list)

[jseager7]

I've added the phenotype terms and experimental condition for trifloxystrobin.

[CuzickA]

Hi @jseager7, please add chemical 'flusilazole' for https://github.com/PHI-base/curation/issues/208

PHIPO normal growth on flusilazole sensitive to flusilazole resistance to flusilazole

PHI-ECO '+ flusilazole'

(note to self: flusilazole is already included in the anti-infective list)

[CuzickA]

Hi @jseager7, please add new chemical terms to PHIPO and PHI-ECO for https://github.com/PHI-base/curation/issues/164

mandipropamid dimethomorph iprovalicarb

(note to self: all three are already included in the anti-infective list)

[jseager7]

I've added phenotype and condition terms for all the above chemicals.

[CuzickA]

Hi @jseager7, please add chemical 'dalfopristin' for https://github.com/PHI-base/curation/issues/159

PHIPO normal growth on dalfopristin sensitive to dalfopristin resistance to dalfopristin

PHI-ECO '+ dalfopristin'

(note to self: dalfopristin is NOT currently included in the anti-infective list. Curation session relates to a bacteria (and antibiotics) and not-fungal species)

[jseager7]

I've added ontology terms for dalfopristin.

[CuzickA]

Hi @jseager7, please add new chemical terms to PHIPO and PHI-ECO for https://github.com/PHI-base/curation/issues/188

thifluzamide penflufen flutolanil

(note to self: all three are already included in the anti-infective list)

[jseager7]

I've added terms for thifluzamide, penflufen, and flutolanil.

[CuzickA]

Hi @jseager7, please add new chemical terms to PHIPO and PHI-ECO for https://github.com/PHI-base/curation/issues/208

imazalil

(note to self: imazalil is already included in the anti-infective list)

[jseager7]

I've added chemical terms for imazalil.

[CuzickA]

Hi @jseager7, when you are available please could you add the PHIPO terms for https://github.com/PHI-base/curation/issues/161

PHIPO normal growth on brefeldin A 3881f5e normal growth on fluconazole a7b1fc1

(note to self: brefeldin A and fluconazole are already included in the anti-infective list)

[CuzickA]

Hi @jseager7, when you are available please could you add the PHIPO terms for PHI-base/curation#161

PHIPO normal growth on brefeldin A normal growth on fluconazole

(note to self: brefeldin A and fluconazole are already included in the anti-infective list)

Hi @jseager7, actually I can probably add these two terms using Protege.

[CuzickA]

Hi @jseager7, when you are available please could you add the PHIPO terms for PHI-base/curation#161 PHIPO normal growth on brefeldin A normal growth on fluconazole (note to self: brefeldin A and fluconazole are already included in the anti-infective list)

Hi @jseager7, actually I can probably add these two terms using Protege.

Terms now made using Protege

[CuzickA]

Hi @jseager7, please add new chemical terms to PHIPO and PHI-ECO for https://github.com/PHI-base/curation/issues/209

Ipconazole

(note to self: Ipconazole is already included in the anti-infective list)

[CuzickA]

Hi @jseager7, please add new chemical terms to PHIPO and PHI-ECO for https://github.com/PHI-base/curation/issues/150

cyprodinil

(note to self: cyprodinil is already included in the anti-infective list)

[jseager7]

I've added chemical terms for ipconazole and cyprodinil.

[CuzickA]

For https://github.com/PHI-base/curation/issues/143

Need to add PHIPO terms normal growth on caspofungin normal growth on terbinafine normal growth on bifonazole

(note to self: all 3 are already included in the anti-infective list)

[CuzickA]

Thanks for adding the above terms @jseager7. I have now used them in PHI-Canto.