Handling Species Specificity
One of the biggest problems for a controlled vocabulary is choosing term names and definitions that will unambiguously identify a component, function or process. If a word or phrase refers to different entities or processes depending upon the organism, subclasses are created based on differentiating characteristics, such structure, physical composition or order of subprocesses, rather than by identifying the taxonomic group in which the component or process occurs.
A classic example of this is cell wall, which refers to the rigid or semi-rigid structure surrounding the cell membrane in plants, fungi and some prokaryotes. Its composition differs between these three sets of organisms, though, so to allow greater specificity of annotation, the ontology describes three subclasses of cell wall differentiated by their physical characteristics:
[i] fungal-type cell wall
[i] peptidoglycan-based cell wall
[i] plant-type cell wall
The definitions for these terms are as follows:
The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan.
plant-type cell wall
A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances.
peptidoglycan-based cell wall
A protective structure outside the cytoplasmic membrane composed of peptidoglycan (also known as murein), a molecule made up of a glycan (sugar) backbone of repetitively alternating N-acetylglucosamine and N-acetylmuramic acid with short, attached, cross-linked peptide chains containing unusual amino acids. An example of this component is found in Escherichia coli. .
fungal-type cell wall
A rigid yet dynamic structure surrounding the plasma membrane that affords protection from stresses and contributes to cell morphogenesis, consisting of extensively cross-linked glycoproteins and carbohydrates. The glycoproteins may be modified with N- or O-linked carbohydrates, or glycosylphosphatidylinositol (GPI) anchors; the polysaccharides are primarily branched glucans, including beta-linked and alpha-linked glucans, and may also include chitin and other carbohydrate polymers, but not cellulose or pectin. Enzymes involved in cell wall biosynthesis are also found in the cell wall. Note that some forms of fungi develop a capsule outside of the cell wall under certain circumstances; this is considered a separate structure.
Note that the definitions use physical and structural characteristics to differentiate between cell wall types.
Terms with Taxon Restrictions
The Gene Ontology also provides an OBO format file containing species-specific terms and the taxa for which they are or are not appropriate. The file can be viewed online , downloaded by FTP , or found in the GO SVN repository at go/quality_control/annotation_checks/taxon_checks/taxon_go_triggers.obo.
The use of sensu, ‘in the sense of’, to designate a certain interpretation of a word or phrase has been deprecated.
[[Category:Ontology]][[Category:GO Editors]] Pascale
Vanaukenk: Vanaukenk moved page Manager Call 2018-10-04 to Manager Call 2018-10-03: Changed to have date coincide with date of the actual call= Meeting URL =
= Agenda =
== Montreal GOC Meeting ==
*Review [http://wiki.geneontology.org/index.php/2018_Montreal_GOC_Meeting_Agenda agenda]
[[Category:GO Consortium]] [[Category:GO Managers Meetings ]] Vanaukenk
Pascale: Created page with " Category:Quality Control"
[[Category:Quality Control]] Pascale
Pascale:Gene products should not be annotated to checkpoint terms based on mutations that result in activation of the checkpoint (i.e, cause cell cycle arrest). Such mutations cause a problem which is detected by the checkpoint sensor, and cell cycle arrest indicates that the checkpoint is functioning normally. This does not represent positive regulation of the checkpoint since the mutated gene is not necessarily part of the checkpoint in a normal cell. Gene products can be annotated to checkpoint terms when a mutation results in inactivation of the checkpoint. This includes, recruiting the checkpoint signalling components, part of the sensor machinery detecting the damage, or any component of the signalling pathway to the effector.
Genes which are involved in correcting the problems detected by the checkpoint should also not be annotated to the checkpoint terms, because they act downstream of the checkpoint. These genes should instead be annotated to "response to checkpoint x" terms, which are in a separate branch of the ontology.
[[Category:Annotation Guidelines]] Pascale
Pascale: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = == Editors Discussion == ===Regulation inference chain=== For Molecular Function, the 'regulat..."= Conference Line =
= Agenda =
== Editors Discussion ==
===Regulation inference chain===
For Molecular Function, the 'regulates' inference chain is a problem.
--- DNA binding transcription factor activity
is_a (has_part?) DNA binding
if we have regulation of DNA binding transcription factor activity
we don't want to say regulation of DNA binding
(the same would be true of DNA binding transcription factor '''regulator''' activity).
* This is true of all MF except for binding.
* Has_part (or another relation) could work if the regulates inference chains stops over it
[[Category: Meetings]] Pascale
Vanaukenk: /* Relations between MF and Input(s) */= Meeting URL =
== Evidence Codes in Noctua ==
*Decision: leave evidence codes as is in Noctua
*Will we continue to use full ECO
*Autocomplete searches perform best when searching on first word in term label, e.g. 'direct' or 'mutant'
== Relations between MF and Input(s) ==
*'has input' vs 'has direct input'
*In GO-CAM models, we are using 'has input' for capturing the objects of MFs
*This is different from conventional annotation where curators sometimes made a distinction between 'has direct input' and 'has input'
*Proposal: replace 'has direct input' with 'has inpu't; obsolete 'has direct input'
*Need to review has_input annotations to remove any extensions that are inconsistent with GO-CAM usage, i.e. an indirect or unknown proximity for an input
*Seth retrieved, as of 2018-07-31, [https://drive.google.com/drive/folders/1TlwrEM2KjAzxIYiCGg0_oicMOYfhiGou all MF annotations] that use has_input in annotation extensions.
*Use cases to discuss:
***Enzymatic modification of a substrate
*Relations Ontology working group (broader than just GO) that is also considering [https://github.com/oborel/obo-relations/issues/244 how to model participants in an MF] and [https://github.com/oborel/obo-relations/issues/171 documentation of has_input and child relations]
= Minutes =
[[Category: Annotation Working Group]] Vanaukenk
Pascale: /* Editors Discussion */= Conference Line =
= Agenda =
== Editors Discussion ==
* Question for Chris: Can we use Sequence Ontology in annotation extensions / has input for GO CAM models ? Needed to continue work on transcription, for eg: https://github.com/geneontology/go-ontology/issues/16152
===Montreal GOC Meeting===
*Add name to attendees list if you're going
===Ontology Developers' workshop===
The meeting will be in Geneva December (8)9-13
* When to book flights and hotel?
* Filling in missing GO-Rhea-Reactome xrefs
** moving from reactions to biochemical pathways
** implementation of a method to keep in synch with all three resources
** GO-CAM templates for pathways??
* GH ticket work and mini-project planning
** Dealing with and migrating binding terms
** Dealing with cellular processes (https://github.com/geneontology/go-ontology/issues/12849)
** Taxon constaints- How do we handle them going forward?
** David H (Can make it)
** Kimberly (Can make it)
** Karen (can NOT make it)
** Harold (Can make it)
** Pascale (Can make it)
** Barbara (Maybe make it)
** Alan B (Rhea, can make any day)
** Anne (Rhea, prefers Monday or Tuesday)
** Peter D (Can make it)
** Paul T (Can make it)
==GH project link==
= Minutes =
[[Category: Meetings]] David