XP:Progress 2008: Difference between revisions
Jump to navigation
Jump to search
(New page: Category:Cross Products) |
(→CHEBI) |
||
(11 intermediate revisions by the same user not shown) | |||
Line 1: | Line 1: | ||
Progress as of 2008/10/20 | |||
== Motivation and Goals == | |||
* GO has become too large and complex to manage manually | |||
* Errors of omission and commission negatively impact users in many ways | |||
* Provide connections between GO and other ontologies | |||
== Methods == | |||
* Create computable logical definitions ([[Cross Products]]) for GO terms using (a) other GO terms (b) terms from other ontologies | |||
* Use logic-based reasoning to find inconsistencies and errors | |||
== Results 2008 == | |||
* We have XP defs for 10712/27589 of GO terms | |||
* 1500-2000 links added or moved in GO based on reasoner results | |||
The table below shows the number of XP defs that have been curated | |||
{|class="wikitable" style="text-align:center border="1" | |||
|+ GO XP Results 2008 | |||
|- | |||
! | |||
! colspan="2" | dynamic | |||
! colspan="4" | spatial | |||
|- | |||
! | |||
! colspan="2" | bioprocess | |||
! colspan="3" | anatomic | |||
! colspan="1" | chemical | |||
|- | |||
! | |||
! biological_process | |||
! molecular_function | |||
! cell | |||
! cellular_component | |||
! uberon | |||
! chebi | |||
|- | |||
! biological_process | |||
| 4133 [http://wiki.geneontology.org/index.php/Regulation_cross-products go_xp_regulation] [http://wiki.geneontology.org/index.php/XP:biological_process_xp_self bp_xp_bp] | |||
| | |||
| 527 [http://wiki.geneontology.org/index.php/XP:biological_process_xp_cell bp_xp_cell] | |||
| 724 [http://wiki.geneontology.org/index.php/XP:biological_process_xp_cellular_component bp_xp_cc] | |||
| 516 [http://wiki.geneontology.org/index.php/XP:biological_process_xp_anatomy bp_xp_uberon] | |||
| 2901 [http://wiki.geneontology.org/index.php/XP:biological_process_xp_chebi bp_xp_chebi] | |||
|- | |||
! molecular_function | |||
| 134 [http://wiki.geneontology.org/index.php/XP:molecular_function_xp_regulators mf_xp_regulators] | |||
| 84 [http://wiki.geneontology.org/index.php/XP:molecular_function_xp_regulators mf_xp_regulators] | |||
| | |||
| | |||
| | |||
| 360 [http://wiki.geneontology.org/index.php/XP:molecular_function_xp_chebi mf_xp_chebi] | |||
|- | |||
! cellular_component | |||
| 24 [http://wiki.geneontology.org/index.php/XP:cellular_component_xp_go cc_xp_go] | |||
| 148 [http://wiki.geneontology.org/index.php/XP:cellular_component_xp_go cc_xp_go] | |||
| | |||
| 715 [http://wiki.geneontology.org/index.php/XP:cellular_component_xp_self cc_xp_cc] | |||
| | |||
| | |||
|} | |||
== Internal Cross Products == | |||
* Cross-products that do not refer to terms outside GO | |||
=== Regulation Cross Products === | |||
* Performed two batch updates on GO, fixing 1000 and 500 links respectively | |||
* Moving towards automation of [[is_a]] link management | |||
=== Cellular Component internal xps (new) === | |||
* New spatial relations: | |||
** surrounded_by | |||
** adjacent_to | |||
=== BP XP CC (new) === | |||
* [[XP:biological_process_xp_cellular_component]] | |||
== External Cross Products == | |||
* Cross-products that refer to terms outside GO | |||
=== Uber Anatomy Ontology (new) === | |||
* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=uberon UBERON page on OBO] | |||
* Multi-species anatomy ontology | |||
* Originally reated to compare phenotype descriptions across species | |||
* [[XP:biological_process_xp_anatomy|Now being used for XPs for GO development terms]] | |||
=== CHEBI === | |||
* [[XP:biological_process_xp_chebi]] | |||
* We are still missing links to many CHEBI terms | |||
** Basic text-matching methods don't work because CHEBI uses different terminological principles from GO | |||
* Pilot project using CHEBI to align GO with pathway dbs | |||
[[Category:Cross Products]] | [[Category:Cross Products]] | ||
=== Cell === | |||
* .. | |||
== Goals for 2009 == | |||
* More curation of XP files | |||
* More automation, better integration with day to day ontology development |
Latest revision as of 18:00, 17 October 2008
Progress as of 2008/10/20
Motivation and Goals
- GO has become too large and complex to manage manually
- Errors of omission and commission negatively impact users in many ways
- Provide connections between GO and other ontologies
Methods
- Create computable logical definitions (Cross Products) for GO terms using (a) other GO terms (b) terms from other ontologies
- Use logic-based reasoning to find inconsistencies and errors
Results 2008
- We have XP defs for 10712/27589 of GO terms
- 1500-2000 links added or moved in GO based on reasoner results
The table below shows the number of XP defs that have been curated
dynamic | spatial | |||||
---|---|---|---|---|---|---|
bioprocess | anatomic | chemical | ||||
biological_process | molecular_function | cell | cellular_component | uberon | chebi | |
biological_process | 4133 go_xp_regulation bp_xp_bp | 527 bp_xp_cell | 724 bp_xp_cc | 516 bp_xp_uberon | 2901 bp_xp_chebi | |
molecular_function | 134 mf_xp_regulators | 84 mf_xp_regulators | 360 mf_xp_chebi | |||
cellular_component | 24 cc_xp_go | 148 cc_xp_go | 715 cc_xp_cc |
Internal Cross Products
- Cross-products that do not refer to terms outside GO
Regulation Cross Products
- Performed two batch updates on GO, fixing 1000 and 500 links respectively
- Moving towards automation of is_a link management
Cellular Component internal xps (new)
- New spatial relations:
- surrounded_by
- adjacent_to
BP XP CC (new)
External Cross Products
- Cross-products that refer to terms outside GO
Uber Anatomy Ontology (new)
- UBERON page on OBO
- Multi-species anatomy ontology
- Originally reated to compare phenotype descriptions across species
- Now being used for XPs for GO development terms
CHEBI
- XP:biological_process_xp_chebi
- We are still missing links to many CHEBI terms
- Basic text-matching methods don't work because CHEBI uses different terminological principles from GO
- Pilot project using CHEBI to align GO with pathway dbs
Cell
- ..
Goals for 2009
- More curation of XP files
- More automation, better integration with day to day ontology development