-
Notifications
You must be signed in to change notification settings - Fork 5
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
New chemical terms #419
Comments
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. |
Thanks, I've now added the PHI-ECO terms to the term creator sheet. |
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
@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. |
@jseager7 In case you want to test the script I will need the following new terms for PHI-base/curation#142 PHIPO PHI-ECO |
- resistance to prothioconazole (PHIPO:0001353) - sensitive to prothioconazole (PHIPO:0001354) - normal growth on prothioconazole (PHIPO:0001355)
@jseager7 please create new terms need for PHI-base/curation#192 PHIPO PHI-ECO (note to self: fluopyram is already included in the anti-infective list) |
- resistance to fluopyram (PHIPO:0001356) - sensitive to fluopyram (PHIPO:0001357) - normal growth on fluopyram (PHIPO:0001358) See #419
@jseager7 please create new terms need for PHI-base/curation#199 PHIPO PHI-ECO (note to self: kresoxim-methyl is already included in the anti-infective list) |
- resistance to kresoxim-methyl (PHIPO:0001359) - sensitive to kresoxim-methyl (PHIPO:0001360) - normal growth on kresoxim-methyl (PHIPO:0001361) See #419
Hi @jseager7, thank you for making these terms. I was having some difficulty finding 'resistance to kresoxim-methyl' in PHI-Canto. When I search for the term id PHIPO:0001359 in PHI-Canto Any ideas as to what has happened here? The other terms are fine. |
@jseager7 For PHI-base/curation#193 Please add PHIPO PHI-ECO (note to self: isopyrazam is already included in the anti-infective list) |
Also for PHI-base/curation#193 Please add PHIPO PHI-ECO (note to self: bixafen is already included in the anti-infective list) |
Also for PHI-base/curation#193 Please add PHIPO |
@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. |
- resistance to isopyrazam (PHIPO:0001362) - sensitive to isopyrazam (PHIPO:0001363) - normal growth on isopyrazam (PHIPO:0001364) See #419
- resistance to bixafen (PHIPO:0001365) - sensitive to bixafen (PHIPO:0001366) - normal growth on bixafen (PHIPO:0001367) See #419
Hi @jseager7 please add the following terms required for PHI-base/curation#182 PHIPO PHI-ECO (note to self: pyrimorph is already included in the anti-infective list) |
- resistance to pyrimorph (PHIPO:0001370) - sensitive to pyrimorph (PHIPO:0001371) - normal growth on pyrimorph (PHIPO:0001372) See #419
@jseager7 For PHI-base/curation#146 Please add PHIPO exact synonym is 'FK506' tacrolimus is already included in PHI-ECO I have asked Jing to add it to the anti-infective list |
- resistance to tacrolimus (PHIPO:0001378) - sensitive to tacrolimus (PHIPO:0001379) - normal growth on tacrolimus (PHIPO:0001380) See #419
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 PHI-ECO (note to self: fenpiclonil is already included in the anti-infective list) |
- resistance to fenpiclonil (PHIPO:0001382) - sensitive to fenpiclonil (PHIPO:0001383) - normal growth on fenpiclonil (PHIPO:0001384) See #419
Fenpiclonil didn't exist in either ontology, so I've added the terms now. |
- resistance to metconazole (PHIPO:0001391) - sensitive to metconazole (PHIPO:0001392) - normal growth on metconazole (PHIPO:0001393) See #419
I've added the phenotype terms and experimental condition for metconazole. |
Hi @jseager7, please add chemical 'trifloxystrobin' for PHI-base/curation#204 PHIPO PHI-ECO (note to self: trifloxystrobin is already included in the anti-infective list) |
- resistance to trifloxystrobin (PHIPO:0001394) - sensitive to trifloxystrobin (PHIPO:0001395) - normal growth on trifloxystrobin (PHIPO:0001396) See #419
I've added the phenotype terms and experimental condition for trifloxystrobin. |
Hi @jseager7, please add chemical 'flusilazole' for PHI-base/curation#208 PHIPO PHI-ECO (note to self: flusilazole is already included in the anti-infective list) |
Hi @jseager7, please add new chemical terms to PHIPO and PHI-ECO for PHI-base/curation#164 mandipropamid (note to self: all three are already included in the anti-infective list) |
- 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
I've added phenotype and condition terms for all the above chemicals. |
Hi @jseager7, please add chemical 'dalfopristin' for PHI-base/curation#159 PHIPO PHI-ECO (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) |
- resistance to dalfopristin (PHIPO:0001411) - sensitive to dalfopristin (PHIPO:0001412) - normal growth on dalfopristin (PHIPO:0001413) See #419
I've added ontology terms for dalfopristin. |
Hi @jseager7, please add new chemical terms to PHIPO and PHI-ECO for PHI-base/curation#188 thifluzamide (note to self: all three are already included in the anti-infective list) |
- 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
I've added terms for thifluzamide, penflufen, and flutolanil. |
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) |
- resistance to imazalil (PHIPO:0001423) - sensitive to imazalil (PHIPO:0001424) - normal growth on imazalil (PHIPO:0001425) See #419
I've added chemical terms for imazalil. |
Hi @jseager7, when you are available please could you add the PHIPO terms for PHI-base/curation#161 PHIPO (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 |
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) |
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) |
- 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
I've added chemical terms for ipconazole and cyprodinil. |
Need to add PHIPO terms (note to self: all 3 are already included in the anti-infective list) |
- normal growth on caspofungin (PHIPO:0001436) - normal growth on terbinafine (PHIPO:0001447) - normal growth on bifonazole (PHIPO:0001448) See #419
Thanks for adding the above terms @jseager7. I have now used them in PHI-Canto. |
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
(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
The text was updated successfully, but these errors were encountered: