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Repository for the Plant Disease Ontology
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Entyloma oryzae (PDO:0000046) #141

Open seymourmegan opened 8 years ago

seymourmegan commented 8 years ago

Entyloma oryzae (PDO:0000046) def'n: A fungal species (PDO:0000069) that causes rice leaf smut (PDO:0000045).

Name Source: Rice Diseases APS NCBI_Taxonomy_ID: TBA EOL: 188781

seymourmegan commented 8 years ago

Entyloma oryzae (PDO:0000046)

phismith commented 8 years ago

Is there only one fungal species that causes rice leaf smut? If yes, then this is not a definition it is a statement about that species. The definition should point to the corresponding taxonomy. If no, then rice leaf smut is not in fact a species, and the definition should read something like:

=def a family of fungal species that ...

BS

On Wed, Sep 2, 2015 at 8:10 PM, Megan Seymour notifications@github.com wrote:

​​ Entyloma oryzae (PDO:0000046)

  • updated NCBITaxon. NCBITaxon: 62636 (genus)
  • updated def'n to include that 'rice leaf smut' is a fungal disease. Old def'n: A fungal species (PDO:0000069) that causes rice leaf smut (PDO:0000045). New def'n: A fungal species (PDO:0000069) that causes rice leaf smut fungal disease (PDO:0000045).

— Reply to this email directly or view it on GitHub https://github.com/Planteome/plant-stress-ontology/issues/141#issuecomment-137277917 .

phismith commented 8 years ago

Is there only one fungal species that causes rice leaf smut? If yes, then this is not a definition it is a statement about that species If no, then the definition should read: BS

On Wed, Sep 2, 2015 at 8:10 PM, Megan Seymour notifications@github.com wrote:

​​ Entyloma oryzae (PDO:0000046)

  • updated NCBITaxon. NCBITaxon: 62636 (genus)
  • updated def'n to include that 'rice leaf smut' is a fungal disease. Old def'n: A fungal species (PDO:0000069) that causes rice leaf smut (PDO:0000045). New def'n: A fungal species (PDO:0000069) that causes rice leaf smut fungal disease (PDO:0000045).

— Reply to this email directly or view it on GitHub https://github.com/Planteome/plant-stress-ontology/issues/141#issuecomment-137277917 .

cmungall commented 8 years ago

Is the plan to move to importing subsets of NCBITaxon (rather than making our own duplicate taxonomy)? In which case we don't need to be manually adding textual definitions at all. NCBITaxon doesn't provide text definitions, but this is fine as we should be encoding the relevant information in edges between classes anyway.

On 3 Sep 2015, at 9:17, Barry Smith wrote:

Is there only one fungal species that causes rice leaf smut? If yes, then this is not a definition it is a statement about that species If no, then the definition should read: BS

On Wed, Sep 2, 2015 at 8:10 PM, Megan Seymour notifications@github.com wrote:

​​ Entyloma oryzae (PDO:0000046)

  • updated NCBITaxon. NCBITaxon: 62636 (genus)
  • updated def'n to include that 'rice leaf smut' is a fungal disease. Old def'n: A fungal species (PDO:0000069) that causes rice leaf smut (PDO:0000045). New def'n: A fungal species (PDO:0000069) that causes rice leaf smut fungal disease (PDO:0000045).

— Reply to this email directly or view it on GitHub https://github.com/Planteome/plant-stress-ontology/issues/141#issuecomment-137277917 .

Reply to this email directly or view it on GitHub: https://github.com/Planteome/plant-stress-ontology/issues/141#issuecomment-137500158

cooperl09 commented 8 years ago

Please remember the PSO is very much in the testing and preliminary stage right now. I am having Megan add the diseases and pathogen sourced from the American Phytopathological Society (http://www.apsnet.org/publications/commonnames/Pages/Rice.aspx).

We are not "creating a taxonomy", but we are resolving some very complex naming issues, using APS, NCBI and the EOL. All the pathogens we are adding are referencing their taxon ids in NCBI.

Once we have a number in, we will import the taxonomy slice that we have created (see https://github.com/Planteome/planteome-ncbi-taxonomy).

cmungall commented 8 years ago

Excellent!

I recommend adding a README.md in the top level of the project with a one or two paragraph description just highlighting project status plans (otherwise I'll keep forgetting and will keep bring up the same issues!)

You can add a readme through the web interface here: https://github.com/Planteome/plant-stress-ontology

On 3 Sep 2015, at 12:23, Laurel Cooper wrote:

Please remember the PSO is very much in the testing and preliminary stage right now. I am having Megan add the diseases and pathogen sourced from the American Phytopathological Society (http://www.apsnet.org/publications/commonnames/Pages/Rice.aspx).

We are not "creating a taxonomy", but we are resolving some very complex naming issues, using APS, NCBI and the EOL. All the pathogens we are adding are referencing their taxon ids in NCBI.

Once we have a number in, we will import the taxonomy slice that we have created (see https://github.com/Planteome/planteome-ncbi-taxonomy).

Reply to this email directly or view it on GitHub: https://github.com/Planteome/plant-stress-ontology/issues/141#issuecomment-137547645