Simplify 'media' in conditions (PHI-ECO) for PHI-Canto curations

[CuzickA]

@ValWood has suggested that we have been capturing more information on the types of experimental media used in the conditions than that of PomBase curators. This may be because with 250+ pathogen species there are a lot of different types of media.

The concern is that it takes more time for the curators to add this level detail and for us to add the requested terms into PHI-ECO.

Talking with @martin2urban today we thought it would be a good idea to reduced the media conditions options down to Minimal medium Rich medium Water medium

and still use 'agar plates' and 'liquid culture' condition terms when relevant to observed phenotype.

Specific types of media could be added as related synonyms or as text comments to the annotation.

Initial notes on media definitions are as follows

Minimal medium Text def: Experiments were performed in defined minimal medium which has just enough ingredients to support growth. (The number of ingredients that must be added to a minimal medium varies enormously depending on which microorganism is being grown). Typically contains a simple carbon source, salts and water. Synonyms: Sucrose nutrient deficient agar (SNA), NO WATER AGAR (keep separate), M9 minimal medium,
Wiki https://en.wikipedia.org/wiki/Growth_medium#Minimal_media

Rich medium: Rich media contain the nutrients required to support the growth of a wide variety of organisms containing complex carbon sources (Sugars, peptides etc). It is an undefined medium that has some complex ingredients, such as yeast extract, which consists of a mixture of many chemicals in unknown proportions. Synonym: complex medium, complete medium, Blood agar, Chocolate agar, Potato dextrose agar (PDA), carboxymethylcellulose medium (CMC) , MacConkey agar, Lowenstein-Jensen medium, trichotoxine induction medium, starch yeast medium, carrot agar, oat meal medium, mung bean medium, yeast extract peptone agar, plant extract agar, potato slice,

[CuzickA]

Current screenshots of PHI-ECO 'grouping growth medium'

[CuzickA]

Add to 'minimal medium' PECO:0005020 text def: Experiments were performed in defined minimal medium which has just enough ingredients to support growth. (The number of ingredients that must be added to a minimal medium varies enormously depending on which microorganism is being grown). Typically contains a simple carbon source, salts and water. exact synonyms: M9 minimal medium, synthetic nutrient-poor agar (SNA)

3a2da30

[CuzickA]

NTR: rich medium PECO:0005031 text def: Rich media contain the nutrients required to support the growth of a wide variety of organisms containing complex carbon sources (Sugars, peptides etc). It is an undefined medium that has some complex ingredients, such as yeast extract, which consists of a mixture of many chemicals in unknown proportions. exact synonyms: numerous as suggested above

16a65e1

[CuzickA]

Next step: to merge and obsolete terms so that only have rich medium minimal medium water medium agar plate liquid culture

[CuzickA]

merge 'carrot medium' PECO:0005026 into 'rich medium' PECO:0005031 143fd41 merge 'complete medium' PECO:0005022 into 'rich medium' PECO:0005031 501260c merge 'potato dextrose medium' PECO:0005021 into 'rich medium' PECO:0005031 ab83e08 merge 'trichothecene biosynthesis medium' PECO:0005025 into 'rich medium' PECO:0005031 8231bd1 merge 'starch yeast medium' PECO:0005023 into 'rich medium' PECO:0005031 f3a0a72 move 'rich medium' PECO:0005031 23a811e merge 'YES' PECO:0000137 into 'rich medium' PECO:0005031 NOT WORKING merge 'YPD' PECO:0000201 into 'rich medium' PECO:0005031 NOT WORKING looks like I cannot merge terms created by Antonia into terms that I have created.

[CuzickA]

@jseager7 please look into IRI changes for PECO to enable merging

[jseager7]

I've fixed this in PHI-ECO now by correcting a lot of absent or incorrect IRI prefixes. From now on, the terms should merge correctly as long as they follow this pattern:

http://purl.obolibrary.org/obo/PECO_0000000

[CuzickA]

'rich medium' has a new id it was PECO:0005031 and is now PECO:0005224 as part of the IRI renaming fix above.

[CuzickA]

merge 'YES' PECO:0000137 into 'rich medium' PECO:0005224 5b687a2 merge 'YPD' PECO:0000201 into 'rich medium' PECO:0005224 d3b7845

merging now working but pay attention to delete duplicate ids, namespaces and creation dates

[CuzickA]

@martin2urban @ValWood I have merged some of the media terms into 'rich medium' as discussed. In the screenshot there are still 8 additional media terms used by the PomBase team but I am pretty sure we have not used them in PHI-Canto yet. The aim is to only have 'rich medium' in this branch. It would be easier for me to obsolete these terms rather than merge them into 'rich medium'. Please could you let me know whether you think it would be ok to obsolete them or if it would be preferable to merge them. The following comment is looking at the 'minimal medium' branch.

[CuzickA]

In this branch we are aiming to have 2 terms 'minimal medium' and 'water medium'. @martin2urban and @ValWood please advise as to whether the remaining terms in this branch could be obsoleted or require merging into 'minimal medium'. Again, I don't think they have been used in PHI-Canto curation sessions so it would be possible to obsolete them (and much quicker).

[ValWood]

@martin2urban will be able to advise better

[martin2urban]

Obsoleting the remaining terms will be fine.

[CuzickA]

obsolete PECO:0000144 PECO:0000136 PECO:0000236 PECO:0000081 PECO:0000162 PECO:0000138 PECO:0000139 PECO:0000148

e58d8a2

[CuzickA]

obsolete PECO:0000073 PECO:0000289 PECO:0000262 PECO:0000126 PECO:0000274 PECO:0000254 PECO:0000331 PECO:0000263 PECO:0000278 PECO:0000286 PECO:0000273 PECO:0000272 PECO:0000264 PECO:0000296 PECO:0000246 PECO:0000276 PECO:0000196 PECO:0000266 PECO:0000054 PECO:0000256 PECO:0000072 PECO:0000016 PECO:0000328 PECO:0000104 PECO:0000230 PECO:0000145 PECO:0000015 PECO:0000147 PECO:0000146

d7834dd

obsolete non-fermentable carbon sources medium PECO:0000213 051ceb3

[CuzickA]

Now looks like this