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New chemical terms #419

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CuzickA opened this issue Aug 7, 2023 · 44 comments
Open

New chemical terms #419

CuzickA opened this issue Aug 7, 2023 · 44 comments
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@CuzickA
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CuzickA commented Aug 7, 2023

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

For PHI-base/curation#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 jseager7 self-assigned this Aug 7, 2023
@jseager7
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jseager7 commented Aug 7, 2023

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
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CuzickA commented Aug 7, 2023

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

jseager7 added a commit that referenced this issue Aug 10, 2023
resistance to triflumizole (PHIPO:0001342)
sensitive to triflumizole (PHIPO:0001343)
normal growth on triflumizole (PHIPO:0001344)
resistance to bitertanol (PHIPO:0001345)
sensitive to bitertanol (PHIPO:0001346)
normal growth on bitertanol (PHIPO:0001347)
resistance to pyrifenox (PHIPO:0001348)
sensitive to pyrifenox (PHIPO:0001349)
normal growth on pyrifenox (PHIPO:0001350)

#419
@jseager7
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@CuzickA I've added the chemical terms to PHIPO and PHI-ECO (see PHI-base/phi-eco@937d8c4) 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
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CuzickA commented Sep 8, 2023

@jseager7 In case you want to test the script I will need the following new terms for PHI-base/curation#142

PHIPO
normal growth on Prothioconazole
sensitive to Prothioconazole
resistance to Prothioconazole

PHI-ECO
'+ Prothioconazole'

jseager7 referenced this issue Sep 11, 2023
- resistance to prothioconazole (PHIPO:0001353)
- sensitive to prothioconazole (PHIPO:0001354)
- normal growth on prothioconazole (PHIPO:0001355)
@CuzickA
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CuzickA commented Sep 26, 2023

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

jseager7 added a commit that referenced this issue Sep 27, 2023
- resistance to fluopyram (PHIPO:0001356)
- sensitive to fluopyram (PHIPO:0001357)
- normal growth on fluopyram (PHIPO:0001358)

See #419
@CuzickA
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CuzickA commented Sep 27, 2023

@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)

jseager7 added a commit that referenced this issue Sep 28, 2023
- resistance to kresoxim-methyl (PHIPO:0001359)
- sensitive to kresoxim-methyl (PHIPO:0001360)
- normal growth on kresoxim-methyl (PHIPO:0001361)

See #419
@CuzickA
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CuzickA commented Sep 29, 2023

@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
image

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

Any ideas as to what has happened here?

The other terms are fine.

@CuzickA
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CuzickA commented Sep 29, 2023

@jseager7 For PHI-base/curation#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
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CuzickA commented Sep 29, 2023

Also for PHI-base/curation#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
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CuzickA commented Sep 29, 2023

Also for PHI-base/curation#193

Please add

PHIPO
normal growth on carboxin

jseager7 added a commit that referenced this issue Oct 2, 2023
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jseager7 commented Oct 2, 2023

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
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CuzickA commented Oct 2, 2023

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.

jseager7 added a commit that referenced this issue Oct 2, 2023
- resistance to isopyrazam (PHIPO:0001362)
- sensitive to isopyrazam (PHIPO:0001363)
- normal growth on isopyrazam (PHIPO:0001364)

See #419
jseager7 added a commit that referenced this issue Oct 2, 2023
- resistance to bixafen (PHIPO:0001365)
- sensitive to bixafen (PHIPO:0001366)
- normal growth on bixafen (PHIPO:0001367)

See #419
jseager7 added a commit that referenced this issue Oct 2, 2023
@CuzickA
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CuzickA commented Oct 10, 2023

Hi @jseager7 please add the following terms required for PHI-base/curation#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)

jseager7 added a commit that referenced this issue Oct 10, 2023
- resistance to pyrimorph (PHIPO:0001370)
- sensitive to pyrimorph (PHIPO:0001371)
- normal growth on pyrimorph (PHIPO:0001372)

See #419
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CuzickA commented Oct 17, 2023

@jseager7 For PHI-base/curation#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

jseager7 added a commit that referenced this issue Oct 17, 2023
- resistance to tacrolimus (PHIPO:0001378)
- sensitive to tacrolimus (PHIPO:0001379)
- normal growth on tacrolimus (PHIPO:0001380)

See #419
@CuzickA
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CuzickA commented Nov 21, 2023

Hi @jseager7 please add the following terms required for PHI-base/curation#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 added a commit that referenced this issue Nov 21, 2023
- resistance to fenpiclonil (PHIPO:0001382)
- sensitive to fenpiclonil (PHIPO:0001383)
- normal growth on fenpiclonil (PHIPO:0001384)

See #419
@jseager7
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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.

jseager7 added a commit that referenced this issue Jan 10, 2024
- resistance to metconazole (PHIPO:0001391)
- sensitive to metconazole (PHIPO:0001392)
- normal growth on metconazole (PHIPO:0001393)

See #419
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I've added the phenotype terms and experimental condition for metconazole.

@CuzickA
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CuzickA commented Jan 19, 2024

Hi @jseager7, please add chemical 'trifloxystrobin' for PHI-base/curation#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 added a commit that referenced this issue Jan 22, 2024
- resistance to trifloxystrobin (PHIPO:0001394)
- sensitive to trifloxystrobin (PHIPO:0001395)
- normal growth on trifloxystrobin (PHIPO:0001396)

See #419
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I've added the phenotype terms and experimental condition for trifloxystrobin.

@CuzickA
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CuzickA commented Jan 30, 2024

Hi @jseager7, please add chemical 'flusilazole' for PHI-base/curation#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)

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CuzickA commented Jan 30, 2024

Hi @jseager7, please add new chemical terms to PHIPO and PHI-ECO for PHI-base/curation#164

mandipropamid
dimethomorph
iprovalicarb

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

jseager7 added a commit that referenced this issue Jan 30, 2024
- resistance to flusilazole (PHIPO:0001399)
- sensitive to flusilazole (PHIPO:0001400)
- normal growth on flusilazole (PHIPO:0001401)
- resistance to mandipropamid (PHIPO:0001402)
- sensitive to mandipropamid (PHIPO:0001403)
- normal growth on mandipropamid (PHIPO:0001404)
- resistance to dimethomorph (PHIPO:0001405)
- sensitive to dimethomorph (PHIPO:0001406)
- normal growth on dimethomorph (PHIPO:0001407)
- resistance to iprovalicarb (PHIPO:0001408)
- sensitive to iprovalicarb (PHIPO:0001409)
- normal growth on iprovalicarb (PHIPO:0001410)

See #419
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I've added phenotype and condition terms for all the above chemicals.

@CuzickA
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CuzickA commented Feb 2, 2024

Hi @jseager7, please add chemical 'dalfopristin' for PHI-base/curation#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 added a commit that referenced this issue Feb 5, 2024
- resistance to dalfopristin (PHIPO:0001411)
- sensitive to dalfopristin (PHIPO:0001412)
- normal growth on dalfopristin (PHIPO:0001413)

See #419
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jseager7 commented Feb 5, 2024

I've added ontology terms for dalfopristin.

@CuzickA
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CuzickA commented Feb 6, 2024

Hi @jseager7, please add new chemical terms to PHIPO and PHI-ECO for PHI-base/curation#188

thifluzamide
penflufen
flutolanil

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

jseager7 added a commit that referenced this issue Feb 7, 2024
- resistance to thifluzamide (PHIPO:0001414)
- sensitive to thifluzamide (PHIPO:0001415)
- normal growth on thifluzamide (PHIPO:0001416)
- resistance to penflufen (PHIPO:0001417)
- sensitive to penflufen (PHIPO:0001418)
- normal growth on penflufen (PHIPO:0001419)
- resistance to flutolanil (PHIPO:0001420)
- sensitive to flutolanil (PHIPO:0001421)
- normal growth on flutolanil (PHIPO:0001422)

See #419
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jseager7 commented Feb 7, 2024

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

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CuzickA commented Feb 9, 2024

Hi @jseager7, please add new chemical terms to PHIPO and PHI-ECO for PHI-base/curation#208

imazalil

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

jseager7 added a commit that referenced this issue Feb 12, 2024
- resistance to imazalil (PHIPO:0001423)
- sensitive to imazalil (PHIPO:0001424)
- normal growth on imazalil (PHIPO:0001425)

See #419
@jseager7
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I've added chemical terms for imazalil.

@CuzickA
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CuzickA commented Mar 12, 2024

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

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CuzickA commented Mar 12, 2024

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 added a commit that referenced this issue Mar 12, 2024
CuzickA added a commit that referenced this issue Mar 12, 2024
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CuzickA commented Mar 12, 2024

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

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CuzickA commented Mar 18, 2024

Hi @jseager7, please add new chemical terms to PHIPO and PHI-ECO for PHI-base/curation#209

Ipconazole

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

@CuzickA
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CuzickA commented Mar 18, 2024

Hi @jseager7, please add new chemical terms to PHIPO and PHI-ECO for PHI-base/curation#150

cyprodinil

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

jseager7 added a commit that referenced this issue Mar 18, 2024
- resistance to ipconazole (PHIPO:0001430)
- sensitive to ipconazole (PHIPO:0001431)
- normal growth on ipconazole (PHIPO:0001432)
- resistance to cyprodinil (PHIPO:0001433)
- sensitive to cyprodinil (PHIPO:0001434)
- normal growth on cyprodinil (PHIPO:0001435)

See #419
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I've added chemical terms for ipconazole and cyprodinil.

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CuzickA commented Mar 27, 2024

For PHI-base/curation#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)

jseager7 added a commit that referenced this issue Mar 27, 2024
- normal growth on caspofungin (PHIPO:0001436)
- normal growth on terbinafine (PHIPO:0001447)
- normal growth on bifonazole (PHIPO:0001448)

See #419
@CuzickA
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CuzickA commented Mar 27, 2024

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

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