Meeting Notes

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February 1st, 2007

Jen Clark, David Hill, Midori Harris, Jane Lomax (8:00am EST- 12:55pm EST)

Strategy ideas:

  1. Maybe we should do all the cell component terms first. Then we can do all other terms that are differentiated by those components.

To do:

  1. Midori to check if peptidoglycans are in cell walls of fungi and to see if there are any that don't have chitin. DONE!
  2. Jen will clean up the plant cell wall terms to indicate that they both contain pectin.
  3. Change cell wall biosynthetic processes to reflect assembly and metabolism. Jane will look into this.
  4. Have Becky confirm that it is ok to change insect aorta to dorsal vessel aorta.(YES)
  5. Is it o.k to say insect appendage development? It is really the only way to distinguish this term. Perhaps we can distinguish *

wings in a more stuctural way. Perhaps arthropod appendage develoment. Exoskeleton-containing appendage development.

  1. We need to rearrange wing development. Q: Does a wing have an exoskeleton?
  2. Check ATP synthesis coupled proton transport in bacteria vs eukaryotes.
  3. Check the pubmed ID from spore wall assembly to (GO:0030476) to get at good defs for the spore wall component terms (Midori).
  4. Ask Michelle about the difference between the eukaryotic and prokaryotic ATP transporters.
  5. As for bacterial capsule, could it be referred to as a semisolid-capsule or gelatious capsule? There is a problem distinguishing this term from its sib which is slime layer. Also need to distinguish it from the fungal capsule. Michelle.
  6. Ask Tanya about the cell surface sensu Magnoliophyta terms. How are they really different from the generic cell surface parent. If not, can we just merge and add a new part of term external side of cell wall.
From meeting minutes, Cambridge, Sept. 2002:
"Cell surface" and related terms: these were added recently by TAIR curators, to capture information from experiments in plants that can narrow down localization to plasma membrane or cell wall but can't distinguish between the two (that's what's meant by "cell surface" in plant literature). The definitions and placement of the cell surface terms were discussed, and changes recommended.
action item 25: TAIR curators to improve definitions of "cell surface" and its children.
    1. Action item: Tanya to review old SF items for cell surface and implement changes suggested if deemed appropriate. Changes suggested are: [DONE 2-20-2007]
      1. merge cell surface and cell surface(s. M.)
      2. create new term 'external side of cell wall' as a part_of child of cell surface
      3. make new term above and is_a child of cell wall part
      4. make 'longitudinal side of cell surface' an is_a child of cell part and remove (s. M.) from main term string (retain as synonym?) leave as part_of child of cell surface
      5. make 'external side of plasma membrane' and is_a child of plasma membrane part
  1. Note that we are using logical "or" in definitions and term names. Make sure this is in the web documentation somewhere.

February 6, 2007

David Hill, Jane Lomax, Jen Clark, Midori Harris (intermittently) 9:30EST-12:30EST

Do the cellular component terms first.

Dealt with

  • cortical microtubules
  • DNA-dependent RNA polymerase, cytosolic, nuclear and plastid
  • Rearranged the thylakoids and their children quite a bit.
  • Did pyruvate dehydrogenases. Made the bacterial one cytosolic.

Action Items:

  1. Do we really need archaebacterial and bacterial cytosolic ribosomes? Ask Harold about how to distinguish these.
  2. Can we obsolete spore wall (sensu Fungi) and make 2 new terms, one to describe the 2-layered pombe and one describing the 4-layered one in cerevisiae. Inform Val et al.
  3. Ask tanya if she is happy with lignin containing spore wall and cellulose containing cell wall.
    1. I consulted with our biochemists and plant primary cell walls have cellulose and pectin while the secondary cell walls have cellulose and lignin. I'm happy with cellulose and pectin-containing cell wall, which is the way you have it now. Do fungal spore walls also have cellulose and pectin? [TB 2-20-07]
  4. Ask Kimberly what the C. elegans dosage compensation complex is composed of. Is it just protein?

February 7, 2007

Jen Clark, Jane Lomax, David Hill

Continue with the component terms.

Dealt with:

  • Changed names of light-harvesting complex sensu terms (ProteoBacteria and Viridiplantae) to plasma membrane light-harversting complex and chloroplast light-harvesting complex
  • proton-transporting ATP synthase complex (sensu Bacteria) -> plasma membrane proton-transporting ATP synthase complex

proton-transporting ATP synthase complex (sensu Eukaryota) -> mitochondrial proton-transporting ATP synthase complex and the same for all child terms

  • When something is in the mitochondrion and in a bacterium, we made the bacterial one cytosolic rather than cytoplasmic to avoid a logical problem with the mitochondrion being a part of the cytoplasm.
  • Renamed and sorted out flagellum terms.

Action items:

  • Ask Michelle to join one of these meetings next week (David)
  • Ask Val to look at the gamma-tubulin terms and then meet by Skype webex (David)
  • Ask Val and Michelle if they can distinguish between the forespore of pombe and the forespore of a bacterium (David)
  • Look into the plasma membrane thylakoid and see exactly what this is. Is it a part of the membrane or is it a vesicle attached to the membrane? (Jen)
  • Get Tanya to deal with the cell surface terms. [DONE! 2-20-2007]

February 8, 2007

David Hill, Jen Clark, Jane Lomax, Michelle Gwinn-Giglio


With Michelle's help try to tackle some of the harder proaryote terms.


  • several terms where locations were in organelles in eukaryotes vs plasma membrane in prokaryotes.

Action Items

  • Michelle to look into capsules and glycocalyx.
  • Jen to look into reaction center as she works through thylakoid.
  • Michelle to look into the periplasmic spaces and what we can call cell-wall bound vs. membrane bound.

Ferbruary 9, 2007


David Hill, Jane Lomax, Jen Clark, Val Wood (intermittently)


  • Val came and helped with the gamma tubulin terms and the prospore/forespore.We did some major rearrangements with the gamma tubulin terms.

Action Items

  • David to look back into eye development and see if we can tidy up the fish vs. mammalian terms.
  • Ask Becky if we can have imaginal disc-derived appendage.(YES)
  • Pombe does not have chitin in its cell wall. We need a term that differentiates the fungal cell wall from the others (plant and bacterial)

February 13, 2007

David Hill, Jane Lomax, Jen Clark, Becky Foulger


  • Try to work on the fly terms.
  • Take care of appendage terms by making them imaginal disc-derived appendages. Clean all terms up.

Action Items

  • Jane to look at dosage compensation complex (assembly) terms. (DONE)
  • Make a generic wing development term to cover non-insect wings.(Jane)
  • Becky to find a distinguishing feature of optic placode in flies.

February 15,2007

David Hill, Jane Lomax, Jane Clark


  • Take care of the eye terms from vertebrates
  • Take care of the thylakoid terms

Action Items

  • Merged the vertebrate terms. There actually is very little difference in mammals and vertebrates.
  • Should cone cell be is_a eye photoreceptor cell differentaiton?(NO, the Drosophila cone cell is not a photoreceptor)
  • Create the correct phycobilosome graph and make different types for cyanelle and plasma membrane derived. (Jen)
  • Look at thylakoid while you are on the subject. (Jen)

February 21,2007

David Hill, Jane Lomax, Jen Clark, Susan Tweedie, Becky Folger


  • Work on more fly terms.
  • Work on embryonic development terms.
  • Work on fly tracheal terms
  • Work on fly male mating behavior terms

Action Items

  • We need to redo all the changes from the 15th. For some reson they did not commit.(done by Jen)
  • e-mail Kimberly about the cuticle terms we would like to change these terms to cuticle formation or cuticle biolgenesis and would like to know if there are clear differences between worm cuticle biogenesis and insect cuticle biogenesis. Same for ecdysis. (structural or process) Yes, there is a clear structural difference. Insect cuticles are chitin-based and worm ones are collage and cuticulin based.(Kimberly)
  • Susan to contact drosophila folks to see if physical orientation is a real male courtship behavior. Emailed Kevin O'Dell (Glasgow) 02/22/07.

February 27,2007

David Hill, Jen Clark, Jane Lomax,


  • Work on the cuticle stuff.
  • Finish eye stuff, cone cells still need to finish photoreceptors.

To Do

  • Jane to change parentage of cuticle biogenesis. (DONE)

March 1,2007

David Hill, Jen Clark, Jane Lomax (With Becky and Michelle for specific questions.)


  • Have a look at the ABC transporters again. May need to reconsider these.
  • Have a look at the cell walls again.

To Do

  • Jen will send an e-mail about annotations to ABC transporters. She will ask people not to move their annotations if they have not moved yet.
  • Jane will send an e-mail to Val about cell walls. We will propose a plan to have a new fungal term to include mannoproteins and glucans and then the existing term and a non-chitin containing term.
  • Jane will finish the cell wall biogenesis terms. (DONE)

March 6,2007

David Hill, Jane Lomax, Jen Clark


  • Fertilization terms.
  • Made a decision on ABC transporter complex. We will keep the merge in place and make two new types, the substrate binding kind and the integrated kind.
  • Merged some of the senescence terms.
  • Changed vacuole terms to reflect the definitions. Plant has no morph change associated with cell cycle and fugal one does.
  • Cuticles are completely done. Differentiated by composition.

To Do

  • Write a sourceforge item on the bacterial vs. eukaryotic chromosomes.(David)
  • Propose the ABC transporter solution terms in SF.Check the synonyms.(Jane)
  • Have a look at modifying the defs fo the dosage compensation complexes.(Jane)
  • Jen and Tanya will look at gamete generation and gametophyte development in plants.(Jen)
  • Try to get Becky for Thursday (Jen).
  • Try to get Michelle and Pascale for the fruiting body terms (Jen).

March 8,2007

David Hill, Becky Foulger, Jen Clark


  • Worked on lots of insect terms with Becky.
    • Merged eptithelial cell differentaiton
    • Renamed gastrulation terms
    • Renamed insect larval terms and pupal terms. Instar larvae and pupa(pupa is only in insect).

To Do

  • Vertebrate gastrulation terms (David)
  • Do we want to obsolete the insect metamorphosis term and split it into two, complete and incomplete? Becky will look at what amphibian larvae are called.
  • Contact Kimberly that they have a gene annotated under pole plasm assembly which is an insect term.
  • Need to come up with a distinguishing feature of the insect chorion and vitelline membrane.(Becky and Susan)
  • Jen will have a look at trichome morphogenesis (sensu magnoliophyta). Right now it is always a part of a leaf. (Jen and Tanya).

March 21, 2007 - Plant Terms

Tanya Berardini, Donghui Li, Jennifer Clark


Worked on the following terms:

GO:0048828 embryonic morphogenesis (sensu Magnoliophyta)

- merged into 'embryonic morphogenesis' (GO:0048598). 

GO:0048233 female gamete generation (sensu Magnoliophyta)

- merged into 'female gametophyte egg cell differentiation' (GO:0009560). 

GO:0009552 gamete generation (sensu Magnoliophyta)

- merged into 'gamete generation' GO:0007276. Renamed GO:0007276 (was gametogenesis, now gamete generation with gametogenesis as synonym). 

GO:0048229 gametophyte development (sensu Magnoliophyta)

- renamed: 'gametophyte development'. 

GO:0048234 male gamete generation (sensu Magnoliophyta)

- merged into 'male gamete generation' (GO:0048232). 

GO:0048235 sperm cell differentiation (sensu Magnoliophyta)

- renamed: 'male gametophyte sperm cell differentiation'. 

GO:0043075 sperm cell nucleus (sensu Magnoliophyta)

- obsolete (prior to this meeting). 

GO:0048236 spore development (sensu Magnoliophyta)

- see action item 3. 

GO:0010069 zygote asymmetric cytokinesis (sensu Magnoliophyta)

- renamed: zygote asymmetric cytokinesis in the embryo sac 

GO:0009919 cytokinesis (sensu Viridiplantae)

- obsolete (prior to this meeting).

Action Items

Action item 1: Tanya

GO:0009971 male meiotic spindle assembly (sensu Viridiplantae) 
and related terms
GO:0007053 male meiotic spindle assembly (sensu Metazoa) 
GO:0007054 male meiosis I spindle assembly (sensu Metazoa)
GO:0007055 male meiosis I spindle assembly (sensu Metazoa)
GO:0007056 female meiotic spindle assembly (sensu Metazoa)
GO:0007057 female meiosis I spindle assembly (sensu Metazoa)
GO:0007058 female meiosis II spindle assembly (sensu Metazoa)

Interestingly, here's what I grabbed from the go_numbers file: (these terms are from the original set of GO ids)

GO:0007053	OS	male meiotic spindle assembly (sensu Drosophila, sensu Mus)
GO:0007054	OS	male meiosis I spindle assembly
GO:0007055	OS	male meiosis II spindle assembly
GO:0007056	OS	female meiotic spindle assembly (sensu Drosophila, sensu Mus)
GO:0007057	OS	female meiosis I spindle assembly
GO:0007058	OS	female meiosis II spindle assembly

Original action item: Need to verify that spindle does form differently in plants. If not merge the above two terms. Leave sensu terms as narrow synonyms.

PMID: 11973272 The Arabidopsis ATK1 gene is required for spindle morphogenesis in male meiosis.

Description of normal spindle formation in male meiosis: (paraphrased) At metaphase I, the spindle has a typical bipolar and highly fusiform configuration, with the chromosomes at the equator. At the conclusion of anaphase I, the interzonal microtubules appear in a tight configuration between the recently separated chromosomes. At telophase I, a broad microtubule structure resembling the phragmoplast forms between two groups of chromosomes. During meiosis II, microtubules between the two groups of chromosomes disappear and two biopolar metaphase II spindles are formed. The spindles then become tightly cylindrical at anaphase II. New microtubule structures than form at telophase II in preparation for cytokinesis.

Note: "These observations during meiosis I and II indicate that the atk1-1 mutant is specifically defective in the formation of the metaphase and anaphase spindles, but did not exhibit an obvious defect in microtubule structures at prophase, nor telophase defects that were independent of the abnormal chromosome distribution." So what exactly does meiotic spindle assembly cover? Do we need child terms for metaphase spindle formation, anaphase spindle formation, etc.? How about spindle maintenance, I don't think the spindle assembles during metaphase, disassembles at the end, then reassembles during anaphase, etc.?

Action item 2: Donghui

GO:0009556 microsporogenesis 
GO:0009554 megasporogenesis 

Need to figure out: is microsporogenesis / megasporogenesis a meiosis (single step)? If so, make these two terms children of 'meiosis' (GO:0007126).

03-22-2007: Both terms should be added as child terms of 'meiosis'.  

Both microspores and megaspores are the products of a meiotic division from microsporocyte or megasporocyte respectively. However, the fate of the four meiotic products differs in microsporogenesis and megasporogenesis.

In microsporogenesis, the microsporocyte undergoes meiotic divisions to produce four meiotic products or microspores. The 4 microspores eventually forms four pollen grains.

In megasporogenesis, four distinct megaspore nuclei develop from the megasporocyte through meiosis. In monosporic or polygonum-type megasporogenesis, only one megaspore, usually that farthest from the micropyle, develops into the embryo sac. The three megaspores towards the micropylar end degenerate. In tetrasporic megasporogenesis, all of the 4 nuclei contribute to the final megagametophyte.

Ref: [1] Molecular genetics of plant development, Stephen Howell, 1998, Cambridge University Press. ISBN 0-521-58784-0. [2] Very nice illustrations.

Action item 3: Jen

GO:0048236 spore development (sensu Magnoliophyta). 

Obsolete this term.

Reason: terms microsporogenesis (GO:0009556, synonym: microspore development) and megasporogenesis (GO:0009554, megaspore development) already exist. No reason to group the two together because the processes are so different. Jen can modify reason if necessary. I (Tanya) think the term was created for lexical grouping instead of biological grouping.

Action item 4: Jen, Tanya, Donghui (next meeting, Wednesday, 3/28, 9:30 am CA, 5:30 pm Cambridge/Hinxton )

Agenda: Clean up gametogenesis and gametophyte development.

Future item: sort out rest of Plant sensu terms

Need Becky Foulger or other fly person to help out. 

Remove the sensu part from the following terms:

GO:0048517    positive regulation of trichome initiation (sensu Magnoliophyta) 
GO:0010091    trichome branching (sensu Magnoliophyta) 
GO:0010026    trichome differentiation (sensu Magnoliophyta) 
GO:0048516    trichome initiation (sensu Magnoliophyta) 
GO:0010090    trichome morphogenesis (sensu Magnoliophyta) 
GO:0048629    trichome patterning (sensu Magnoliophyta) 
GO:0002226    innate immune response (sensu Viridiplantae) [DONE - 3/27-07 - JC and AD]
GO:0002219    activation of innate immune response (sensu Viridiplantae) [DONE - 3/27-07 - JC and AD]


March 27, 2007 - Plant Immune Terms

Alex Diehl, Jennifer Clark

We fixed:

activation of innate immune response (sensu Viridiplantae)
innate immune response (sensu Viridiplantae)

just by merging with the parent term.

There are a number of other non-plant immune terms and I have sent a list of them to Alex. He is going to have a think about them and get back to me when there's a good moment for a conference call to sort them out.

March 28, 2007 - female gametophyte development and related terms

Tanya Berardini, Donghui Li, Jennifer Clark


Worked on 'female gametophyte development' and its child terms.

female gametophyte development

- Replaced the term name 'female gametophyte development' with 'embryo sac development'. - Included 'female gametophyte development' as a synonym of 'embryo sac development'.

Created a separate term 'megagametogenesis' (GO:0009561).
Regrouped the child terms of 'embryo sac development' into 'megagametogeneis' and 'megasporogenesis'.

'megagametogenesis' was previously used as a synonym to 'female gametophyte development' (or embryo sac development). We have adopted the definitions by Howell (1998, Molecular Genetics of Plant Development, Cambridge University Press, ISBN 0-521-58784-0) and divided 'embryo sac development' into 'megasporogenesis' (refering to the formation of megaspores from megasporocyte) and 'megagametogenesis' (from megaspores to embryo sac).

antipodal cell differentiation (GO:0009557)

Unchanged. Now a child of 'megagametogenesis'.

cellularization of megagametophyte (GO:0009558)

New and improved definition. Now a child of 'megagametogenesis'.

female gametophyte central cell differentiation (GO:0009559)

Renamed: embryo sac central cell differentiation to be consistent with 'embryo sac development' and other related terms. New definition.

Action Items