Ontology Structure: Difference between revisions
mNo edit summary |
|||
(8 intermediate revisions by 3 users not shown) | |||
Line 1: | Line 1: | ||
[[Category:Ontology]] [[Category:GO Consortium Meetings]] | |||
Note: this page may get merged with [[Ontology_Development]] | Note: this page may get merged with [[Ontology_Development]] | ||
Line 5: | Line 6: | ||
DONE | DONE | ||
== | == ''disjoint_from'' links == | ||
3 terms in GO are no declared mutually disjoint: | |||
CP, MCOP, MOP | |||
Could be done for 3 root nodes | |||
Also for other higher level terms | |||
== Create separate editorial version of ontology == | |||
This | This page has moved: | ||
[[Ontology_CVS_Directory_Layout_Overhaul]] | |||
== Ontology linking and cross-products == | == Ontology linking and cross-products == | ||
Line 58: | Line 49: | ||
OBO-Edit is capable of handling these links | OBO-Edit is capable of handling these links | ||
[[Image:hd-complex.jpg]] | |||
===== AmiGO ===== | ===== AmiGO ===== | ||
Line 86: | Line 79: | ||
We have added a [[Cross_Product_Guide]], intended to answer all your questions about cross-products | We have added a [[Cross_Product_Guide]], intended to answer all your questions about cross-products | ||
==== biological_process_xp_cell ==== | ==== biological_process_xp_cell ==== | ||
CL is currently undergoing rennovation. However, the CL cross-products can still be edited and used. | |||
[[Cell cross-products]] | [[Cell cross-products]] | ||
==== biological_process_xp_chebi ==== | ==== biological_process_xp_chebi ==== | ||
Initial set by mike Bada | |||
[[Chebi cross-products]] | [[Chebi cross-products]] | ||
Ongoing issues: | |||
* plurals in ChEBI | |||
* roles in chebi | |||
* unusual DAG structure | |||
==== Others ==== | |||
[http://www.berkeleybop.org/obol Obol] |
Latest revision as of 11:54, 14 March 2019
Note: this page may get merged with Ontology_Development
is_a completeness
DONE
disjoint_from links
3 terms in GO are no declared mutually disjoint:
CP, MCOP, MOP
Could be done for 3 root nodes
Also for other higher level terms
Create separate editorial version of ontology
This page has moved: Ontology_CVS_Directory_Layout_Overhaul
Ontology linking and cross-products
Internal (Intra-GO) links
GO currently has links within the 3 ontologies, but not between
Biological process to molecular function
Cellular component to molecular function
Implementation
Links spanning the 3 ontologies do not differ significantly from existing DAG links. We could thus include them in the main GO file. However, users expectations will be violated - annotations cannot be propagated up these links in the same way. For this reason it may be better to capture these links in a separate file; for example:
go/ ontology/ gene_ontology_editorial.obo function_to_process.obo component_to_function.obo
OBO-Edit
OBO-Edit is capable of handling these links
AmiGO
Internal cross-products
Regulation cross-products
Other internal cross-products
External DAG links
External DAG links are different from external XPs. A DAG link is just a simple link that happens to span two ontologies.
Examples: between microvillus and hair cell
External cross-products
Cross-product meetings: [1]
We have added a Cross_Product_Guide, intended to answer all your questions about cross-products
biological_process_xp_cell
CL is currently undergoing rennovation. However, the CL cross-products can still be edited and used.
biological_process_xp_chebi
Initial set by mike Bada
Ongoing issues:
- plurals in ChEBI
- roles in chebi
- unusual DAG structure