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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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reorganization of the 'chromosome' branch #672

Closed gocentral closed 9 years ago

gocentral commented 21 years ago

There's been some confusion about which terms to use for when (ie, 'interphase chromosome' vs 'nuclear chromosome') and terms not mapping up to the correct parent (ie, 'nucleosome' and 'telomere' not a child of 'nucleus').

So I'm working on making sure there is correct parentage & the distinctions between different types of chromosomes are clear.
All children of the term 'chromosome' (goid:5694) will be looked at.

Just giving you a heads up for what's coming. I'll post it to the list when the proposal is ready.

Reported by: eurie

Original Ticket: "geneontology/ontology-requests/673":https://sourceforge.net/p/geneontology/ontology-requests/673

gocentral commented 21 years ago

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These biological issues need to be presented in the ontology:

  1. Location of chromosome in prokaryotes vs eukaryotes
  2. Chromosomes are dynamic - they condense & decondense & are present in different states (and different proteins might be decorated on the chromsome at such different times)
  3. Difference in the status of the nuclear membrane during mitosis. An 'open mitosis' vs 'closed mitosis' (ie, breakdown of the nuclear
    membrane in mammalian cells while the nuclear membrane remains intact in yeast).

How these issues were addressed:

  1. Set up the structure so that there are generic chromosome terms that can have 'cytoplasmic' and 'nuclear' terms as children. It makes it a little unwieldy to look at all at once but it's flexible enough to accommodate prokaryotes that have nucleosomes and stuff.
  2. Different children of 'chromosome' describe the different states - 'chromatin' has remained to describe the general decondensed chromosome that is present in non-dividing cells. 'condensed chromosome' describes chromosomes that are undergoing mitosis and meiosis.
  3. 'condensed chromosome' has a child 'condensed nuclear chromosome' - the 'condensed chromosome' maps up to 'intracellular' while 'nuclear condensed chromosome' maps up to 'nucleus'. therefore, fungal gene products that decorate the mitotic chromosome can annotate to terms listed under 'condensed nuclear chromosome' while mammalian gene products that decorate the mitotic chromosome can annotate to terms listed under 'condensed chromosome' and not worry about true path violations.

<intracellular; goid:5622 <chromosome; goid:5694 <origin of replication recognition complex %cytoplasmic origin of replication recognition complex %nuclear origin of replication recognition complex <pericentric region of the chromosome <kinetochore %condensed chromosome kinetochore %condensed nuclear chromosome kinetochore %pericentric region of the condensed chromosome <condensed chromosome kinetochore %pericentric region of the condensed nuclear chromosome <condensed nuclear chromosome kinetochore <telomeric region of the chromosome <telomere cap complex %nuclear telomere cap complex %telomeric region of the nuclear chromosome <nuclear telomere cap complex <nuclear telomeric heterochromatin; goid:5724 <provirus; goid:19038 <chromatin <nucleosome %cytoplasmic nucleosome %nuclear nucleosome
%cytoplasmic chromatin <cytoplasmic nucleosome %nuclear chromatin <perichromatin fibrils; goid:5726 <nuclear nucleosome %nuclear euchromatin %nuclear heterochromatin %euchromatin %nuclear euchromatin; goid:5719 %heterochromatin %nuclear heterochromatin; goid:5720 %all children %condensed chromosome <pericentric region of the condensed chromosome <cohesion complex; goid:8278 <cohesion core heterodimer; goid:8280 %nuclear cohesin complex <condensin complex <condensin core heterodimer %nuclear condensin complex %condensed nuclear chromosome %cytoplasmic chromosome; goid:229 <cytoplasmic chromatin <cytoplasmic origin of replication recognition complex %nuclear chromosome; goid:228 <nuclear chromatin <nuclear origin of replication recognition complex %telomeric region of the nuclear chromosome %condensed nuclear chromosome <pericentric region of the condensed nuclear chromosome <nuclear cohesin complex <nuclear condensin complex <synaptonemal complex <lateral element (syn:axial element) <central element <transverse filament <chiasma; goid:5712 (syn:chiasmata) <recombination nodule; goid:5713 %early recombination nodule; goid:5714 %late recombination nodule; goid:5715 %nuclear sex chromosome %mitochondrial chromosome; goid:262 %plastid chromosome; goid:9508 %polytene chromosome; goid:5700 %sex chromosome %nuclear sex chromosome %W chromosome %X chromosome %Barr body %Y chromosome %Z chromosome <sex chromatin; goid:1739 <nucleus; goid:5634 <telomerase holoenzyme complex; goid:5697 %telomerase catalytic core complex; goid:333 <nuclear chromosome; goid:228 <cytoplasm; goid:5737 <cytoplasmic chromosome; goid:229

moves: 'telomerase holoenzyme complex' should not be a part of 'telomere' because it is not ALWAYS associated at the telomere.

change term string name: euchromatin; goid:5719 - to 'nuclear euchromatin' heterochromatin; goid:5720 - to 'nuclear heterochromatin' telomeric heterochromatin; goid:5724 - to 'nuclear telomeric heterochromatin'

obsolete because they belong in the sequence ontology. centromere; goid:5698 telomere; goid:5696

obsolete because the difference between these terms and 'chromosome' is based on temporal divisions or process division. chromatid; goid:5695 cytoplasmic interphase chromosome; goid:233 cytoplasmic mitotic chromosome; goid:231 interphase chromosome; goid:5707 nuclear interphase chromosome; goid:232 meiotic chromosome; goid:5711 mitotic chromosome; goid:5708 metaphase chromosome; goid:5710 nuclear mitotic chromosome; goid:230 prophase chromosome; goid:5709

obsolete & create terms with the same text string because the definitions are way too specific. chromatin; goid:5717 condensin complex; goid:5676 condensin core heterodimer; goid:8621 nucleosome; goid:5718 kinetochore; goid:5699

obsolete because definition is not quite true for all organisms - SC may or may not promotes genetic recombination, depending on the organism.
synaptonemal complex; goid:5716

Original comment by: eurie

gocentral commented 21 years ago

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comments sent to mailing list:

comments on terms: I particularly like the 'condensed chromosome' terms.

- I would leave 'the' out of terms names (e.g. pericentric region of the chromosome --> pericentric region of chromosome, or even chromosome, pericentric region).

- The existing GO:0008278 and GO:0008280 say 'cohesin complex,' not 'cohesion' as in the draft - is this a deliberate change or a typo?

- I think the W, X, Y, and Z chromosomes should go directly under sex chromosome, since they can be nuclear or cytoplasmic (the latter during mitosis, same as autosomes in species that do open mitosis).

- I'm assuming that all of the terms shown without IDs in the ontology portion will get new IDs. But there are a few anomalies, raising the next few questions:

- Will you use the existing ID for Barr body (GO:0001740)?

- Will the reworded term keep the same ID as the existing 'origin recognition complex' (GO:0005664)? Either way, it should keep the synonym 'ORC.' (or, if the new term is supposed to be more general than GO:0005664, 5664 could become a 'sensu Eukarya' term ... I want to keep the 'ORC' synonym for searching if at all possible)

- Ought we not replace synaptonemal complex (5716) with a new ID & identical string? It's not on the list of terms to be replaced - instead it says to obsolete but doesn't say to replace, but you show the term without an ID in the ontology draft.

comments on definitions: > term: telomeric region of the chromosome > definition: The terminal region of a chromosome that includes the > telomeric DNA repeats and associated proteins.

I would use the phrase 'linear chromosome' in defs of all telomere-related terms so for this & next few I suggest:

The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.

> term: telomeric region of the nuclear chromosome

The terminal region of a linear chromosome in the nucleus that includes the telomeric DNA repeats and associated proteins.

> term: telomere cap complex

A complex of DNA and protein located at the end of a linear chromosome that protects and stabilizes the chromosome.

> term: nuclear telomere cap complex

A complex of DNA and protein located at the end of a linear chromosome in the nucleus that protects and stabilizes the chromosome.

> term: chromatin > definition: The ordered and organized complex of DNA and protein that > is part of the chromosome.

'... forms the chromosome' sounds better than 'is part of the chromosome.' Same would go for nuclear chromatin & cytoplasmic chromatin defs.

> term: euchromatin > definition: A dispersed and less dense dense form of chromatin.

The 'less dense' bit makes me expect to see something more (i.e. less dense than what?). Perhaps change the wording; how about 'A dispersed, relatively uncompacted form of chromatin'?

> term: heterochromatin > definition: A compact and more condensed form of chromatin.

Change to: A compact and highly condensed form of chromatin

> term: nucleosome > definition: A complex comprised of DNA wound around a multi-subunit > core and associated proteins. Together the complex forms the primary > packing unit of DNA into higher order structures.

'Together the complex ...' sounds odd - change to 'A complex composed of DNA wound around a multi-subunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.'

Change cytoplasmic nucleosome and nuclear nucleosome defs accordingly.

Midori

Original comment by: mah11

gocentral commented 21 years ago

Original comment by: eurie