/cell-ontology

New issue

Cede fungal cell types to FAO #447

Open
cmungall opened this Issue Sep 22, 2016 · 4 comments

Comments

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
2 participants
@cmungall @dianeoinglis
@cmungall
Owner

cmungall commented Sep 22, 2016

cc @ukemi, @dianeoinglis @dosumis

first do a gap analysis and see what's missing, then fix GO

This was referenced Sep 22, 2016

Closed
Open
Closed
@dianeoinglis

dianeoinglis commented Oct 18, 2016 • edited

Add NTR 'substrate mycelium formation' geneontology/go-ontology#12742 to this list.
@dianeoinglis

dianeoinglis commented Oct 18, 2016

@cmungall
Is there a script or program for gap analysis?
@cmungall
Owner

cmungall commented Oct 18, 2016

Not really an off the shelf thing. I was going to run a basic alignment and post the results here
@cmungall
Owner

cmungall commented Oct 18, 2016

may be easy to do manually

image:

f

tree

 / BFO:0000002 ! continuant
  is_a BFO:0000004 ! independent continuant
   is_a BFO:0000040 ! material entity
    is_a CARO:0000006 ! material anatomical entity
     is_a CARO:0000003 ! anatomical structure
      is_a CL:0000000 ! cell
       is_a CL:0000003 ! native cell
        is_a CL:0000255 ! eukaryotic cell
         is_a CL:0000521 ! fungal cell *** 
          is_a CL:0000286 ! hyphal cell
          is_a CL:0000334 ! vegetative cell (sensu Fungi)
          is_a CL:0000600 ! heterokaryon
           is_a CL:0000603 ! dikaryon
          is_a CL:0002369 ! fungal spore
           is_a CL:0000596 ! sexual spore
            is_a CL:0000607 ! ascospore
            is_a CL:0000608 ! zygospore
            is_a CL:0000615 ! basidiospore
           is_a CL:0000605 ! fungal asexual spore
            is_a CL:0000599 ! conidium
             is_a CL:0000606 ! macroconidium
              is_a CL:0002384 ! uninucleate macroconidium
               is_a CL:0002389 ! uninucleate arthroconidium
               is_a CL:0002390 ! uninucleate blastconidium
              is_a CL:0002385 ! blastoconidium
               is_a CL:0002390 ! uninucleate blastconidium
               is_a CL:0002391 ! multinucleate blastoconidium
              is_a CL:0002386 ! multinucleate macroconidium
               is_a CL:0002388 ! multinucleate arthroconidium
               is_a CL:0002391 ! multinucleate blastoconidium
              is_a CL:0002387 ! arthroconidium
               is_a CL:0002388 ! multinucleate arthroconidium
               is_a CL:0002389 ! uninucleate arthroconidium
             is_a CL:0002381 ! uninucleate conidium
              is_a CL:0000597 ! microconidium
              is_a CL:0002383 ! conidium of conidiophore head
              is_a CL:0002384 ! uninucleate macroconidium
               is_a CL:0002389 ! uninucleate arthroconidium
               is_a CL:0002390 ! uninucleate blastconidium
             is_a CL:0002382 ! multinucleate conidium
              is_a CL:0002386 ! multinucleate macroconidium
               is_a CL:0002388 ! multinucleate arthroconidium
               is_a CL:0002391 ! multinucleate blastoconidium
            is_a CL:0000726 ! chlamydospore
            is_a CL:0002380 ! oospore
          is_a CL:0002674 ! H minus
          is_a CL:0002675 ! H plus
      is_a GO:0005623 ! cell
       equivalent CL:0000000 ! cell
        is_a CL:0000003 ! native cell
         is_a CL:0000255 ! eukaryotic cell
          is_a CL:0000521 ! fungal cell *** 
           is_a CL:0000286 ! hyphal cell
           is_a CL:0000334 ! vegetative cell (sensu Fungi)
           is_a CL:0000600 ! heterokaryon
            is_a CL:0000603 ! dikaryon
           is_a CL:0002369 ! fungal spore
            is_a CL:0000596 ! sexual spore
             is_a CL:0000607 ! ascospore
             is_a CL:0000608 ! zygospore
             is_a CL:0000615 ! basidiospore
            is_a CL:0000605 ! fungal asexual spore
             is_a CL:0000599 ! conidium
              is_a CL:0000606 ! macroconidium
               is_a CL:0002384 ! uninucleate macroconidium
                is_a CL:0002389 ! uninucleate arthroconidium
                is_a CL:0002390 ! uninucleate blastconidium
               is_a CL:0002385 ! blastoconidium
                is_a CL:0002390 ! uninucleate blastconidium
                is_a CL:0002391 ! multinucleate blastoconidium
               is_a CL:0002386 ! multinucleate macroconidium
                is_a CL:0002388 ! multinucleate arthroconidium
                is_a CL:0002391 ! multinucleate blastoconidium
               is_a CL:0002387 ! arthroconidium
                is_a CL:0002388 ! multinucleate arthroconidium
                is_a CL:0002389 ! uninucleate arthroconidium
              is_a CL:0002381 ! uninucleate conidium
               is_a CL:0000597 ! microconidium
               is_a CL:0002383 ! conidium of conidiophore head
               is_a CL:0002384 ! uninucleate macroconidium
                is_a CL:0002389 ! uninucleate arthroconidium
                is_a CL:0002390 ! uninucleate blastconidium
              is_a CL:0002382 ! multinucleate conidium
               is_a CL:0002386 ! multinucleate macroconidium
                is_a CL:0002388 ! multinucleate arthroconidium
                is_a CL:0002391 ! multinucleate blastoconidium
             is_a CL:0000726 ! chlamydospore
             is_a CL:0002380 ! oospore
           is_a CL:0002674 ! H minus
           is_a CL:0002675 ! H plus
       is_a CL:0000003 ! native cell
        is_a CL:0000255 ! eukaryotic cell
         is_a CL:0000521 ! fungal cell *** 
          is_a CL:0000286 ! hyphal cell
          is_a CL:0000334 ! vegetative cell (sensu Fungi)
          is_a CL:0000600 ! heterokaryon
           is_a CL:0000603 ! dikaryon
          is_a CL:0002369 ! fungal spore
           is_a CL:0000596 ! sexual spore
            is_a CL:0000607 ! ascospore
            is_a CL:0000608 ! zygospore
            is_a CL:0000615 ! basidiospore
           is_a CL:0000605 ! fungal asexual spore
            is_a CL:0000599 ! conidium
             is_a CL:0000606 ! macroconidium
              is_a CL:0002384 ! uninucleate macroconidium
               is_a CL:0002389 ! uninucleate arthroconidium
               is_a CL:0002390 ! uninucleate blastconidium
              is_a CL:0002385 ! blastoconidium
               is_a CL:0002390 ! uninucleate blastconidium
               is_a CL:0002391 ! multinucleate blastoconidium
              is_a CL:0002386 ! multinucleate macroconidium
               is_a CL:0002388 ! multinucleate arthroconidium
               is_a CL:0002391 ! multinucleate blastoconidium
              is_a CL:0002387 ! arthroconidium
               is_a CL:0002388 ! multinucleate arthroconidium
               is_a CL:0002389 ! uninucleate arthroconidium
             is_a CL:0002381 ! uninucleate conidium
              is_a CL:0000597 ! microconidium
              is_a CL:0002383 ! conidium of conidiophore head
              is_a CL:0002384 ! uninucleate macroconidium
               is_a CL:0002389 ! uninucleate arthroconidium
               is_a CL:0002390 ! uninucleate blastconidium
             is_a CL:0002382 ! multinucleate conidium
              is_a CL:0002386 ! multinucleate macroconidium
               is_a CL:0002388 ! multinucleate arthroconidium
               is_a CL:0002391 ! multinucleate blastoconidium
            is_a CL:0000726 ! chlamydospore
            is_a CL:0002380 ! oospore
          is_a CL:0002674 ! H minus
          is_a CL:0002675 ! H plus
 / GO:0005575 ! cellular_component
  is_a CL:0000000 ! cell
   is_a CL:0000003 ! native cell
    is_a CL:0000255 ! eukaryotic cell
     is_a CL:0000521 ! fungal cell *** 
      is_a CL:0000286 ! hyphal cell
      is_a CL:0000334 ! vegetative cell (sensu Fungi)
      is_a CL:0000600 ! heterokaryon
       is_a CL:0000603 ! dikaryon
      is_a CL:0002369 ! fungal spore
       is_a CL:0000596 ! sexual spore
        is_a CL:0000607 ! ascospore
        is_a CL:0000608 ! zygospore
        is_a CL:0000615 ! basidiospore
       is_a CL:0000605 ! fungal asexual spore
        is_a CL:0000599 ! conidium
         is_a CL:0000606 ! macroconidium
          is_a CL:0002384 ! uninucleate macroconidium
           is_a CL:0002389 ! uninucleate arthroconidium
           is_a CL:0002390 ! uninucleate blastconidium
          is_a CL:0002385 ! blastoconidium
           is_a CL:0002390 ! uninucleate blastconidium
           is_a CL:0002391 ! multinucleate blastoconidium
          is_a CL:0002386 ! multinucleate macroconidium
           is_a CL:0002388 ! multinucleate arthroconidium
           is_a CL:0002391 ! multinucleate blastoconidium
          is_a CL:0002387 ! arthroconidium
           is_a CL:0002388 ! multinucleate arthroconidium
           is_a CL:0002389 ! uninucleate arthroconidium
         is_a CL:0002381 ! uninucleate conidium
          is_a CL:0000597 ! microconidium
          is_a CL:0002383 ! conidium of conidiophore head
          is_a CL:0002384 ! uninucleate macroconidium
           is_a CL:0002389 ! uninucleate arthroconidium
           is_a CL:0002390 ! uninucleate blastconidium
         is_a CL:0002382 ! multinucleate conidium
          is_a CL:0002386 ! multinucleate macroconidium
           is_a CL:0002388 ! multinucleate arthroconidium
           is_a CL:0002391 ! multinucleate blastoconidium
        is_a CL:0000726 ! chlamydospore
        is_a CL:0002380 ! oospore
      is_a CL:0002674 ! H minus
      is_a CL:0002675 ! H plus
  is_a GO:0005623 ! cell
   equivalent CL:0000000 ! cell
    is_a CL:0000003 ! native cell
     is_a CL:0000255 ! eukaryotic cell
      is_a CL:0000521 ! fungal cell *** 
       is_a CL:0000286 ! hyphal cell
       is_a CL:0000334 ! vegetative cell (sensu Fungi)
       is_a CL:0000600 ! heterokaryon
        is_a CL:0000603 ! dikaryon
       is_a CL:0002369 ! fungal spore
        is_a CL:0000596 ! sexual spore
         is_a CL:0000607 ! ascospore
         is_a CL:0000608 ! zygospore
         is_a CL:0000615 ! basidiospore
        is_a CL:0000605 ! fungal asexual spore
         is_a CL:0000599 ! conidium
          is_a CL:0000606 ! macroconidium
           is_a CL:0002384 ! uninucleate macroconidium
            is_a CL:0002389 ! uninucleate arthroconidium
            is_a CL:0002390 ! uninucleate blastconidium
           is_a CL:0002385 ! blastoconidium
            is_a CL:0002390 ! uninucleate blastconidium
            is_a CL:0002391 ! multinucleate blastoconidium
           is_a CL:0002386 ! multinucleate macroconidium
            is_a CL:0002388 ! multinucleate arthroconidium
            is_a CL:0002391 ! multinucleate blastoconidium
           is_a CL:0002387 ! arthroconidium
            is_a CL:0002388 ! multinucleate arthroconidium
            is_a CL:0002389 ! uninucleate arthroconidium
          is_a CL:0002381 ! uninucleate conidium
           is_a CL:0000597 ! microconidium
           is_a CL:0002383 ! conidium of conidiophore head
           is_a CL:0002384 ! uninucleate macroconidium
            is_a CL:0002389 ! uninucleate arthroconidium
            is_a CL:0002390 ! uninucleate blastconidium
          is_a CL:0002382 ! multinucleate conidium
           is_a CL:0002386 ! multinucleate macroconidium
            is_a CL:0002388 ! multinucleate arthroconidium
            is_a CL:0002391 ! multinucleate blastoconidium
         is_a CL:0000726 ! chlamydospore
         is_a CL:0002380 ! oospore
       is_a CL:0002674 ! H minus
       is_a CL:0002675 ! H plus
   is_a CL:0000003 ! native cell
    is_a CL:0000255 ! eukaryotic cell
     is_a CL:0000521 ! fungal cell *** 
      is_a CL:0000286 ! hyphal cell
      is_a CL:0000334 ! vegetative cell (sensu Fungi)
      is_a CL:0000600 ! heterokaryon
       is_a CL:0000603 ! dikaryon
      is_a CL:0002369 ! fungal spore
       is_a CL:0000596 ! sexual spore
        is_a CL:0000607 ! ascospore
        is_a CL:0000608 ! zygospore
        is_a CL:0000615 ! basidiospore
       is_a CL:0000605 ! fungal asexual spore
        is_a CL:0000599 ! conidium
         is_a CL:0000606 ! macroconidium
          is_a CL:0002384 ! uninucleate macroconidium
           is_a CL:0002389 ! uninucleate arthroconidium
           is_a CL:0002390 ! uninucleate blastconidium
          is_a CL:0002385 ! blastoconidium
           is_a CL:0002390 ! uninucleate blastconidium
           is_a CL:0002391 ! multinucleate blastoconidium
          is_a CL:0002386 ! multinucleate macroconidium
           is_a CL:0002388 ! multinucleate arthroconidium
           is_a CL:0002391 ! multinucleate blastoconidium
          is_a CL:0002387 ! arthroconidium
           is_a CL:0002388 ! multinucleate arthroconidium
           is_a CL:0002389 ! uninucleate arthroconidium
         is_a CL:0002381 ! uninucleate conidium
          is_a CL:0000597 ! microconidium
          is_a CL:0002383 ! conidium of conidiophore head
          is_a CL:0002384 ! uninucleate macroconidium
           is_a CL:0002389 ! uninucleate arthroconidium
           is_a CL:0002390 ! uninucleate blastconidium
         is_a CL:0002382 ! multinucleate conidium
          is_a CL:0002386 ! multinucleate macroconidium
           is_a CL:0002388 ! multinucleate arthroconidium
           is_a CL:0002391 ! multinucleate blastoconidium
        is_a CL:0000726 ! chlamydospore
        is_a CL:0002380 ! oospore
      is_a CL:0002674 ! H minus
      is_a CL:0002675 ! H plus
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment