Ontology Structure: Difference between revisions

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

Function-Process_Links

Cellular component to molecular function

go/scratch/obol_results/cellular_component_links_to_molecular_function.obo

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

AmiGO:Inter-ontology_links

Internal cross-products

Regulation cross-products

Regulation_cross-products

Other internal cross-products

go/scratch/obol_results/biological_process_xp_cell-obol.obo

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.

Cell cross-products

biological_process_xp_chebi

Initial set by mike Bada

Chebi cross-products

Ongoing issues:

plurals in ChEBI
roles in chebi
unusual DAG structure

Others

Obol

@@ Line 1: / Line 1: @@
+[[Category:Ontology]] [[Category:GO Consortium Meetings]]
 Note: this page may get merged with [[Ontology_Development]]
@@ Line 4: / Line 5: @@
 DONE
+== ''disjoint_from'' links ==
+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 ==
-Purpose: provide buffer between ontology users and editors to allow implementation of new features in a way that is non-disruptive
+This page has moved:
+[[Ontology_CVS_Directory_Layout_Overhaul]]
-Currently we have
+== Ontology linking and cross-products ==
-  go/
+=== Internal (Intra-GO) links ===
-    ontology/
-      gene_ontology.obo
+GO currently has links within the 3 ontologies, but not between
-      gene_ontology_edit.obo
+==== Biological process to molecular function ====
+[[Function-Process_Links]]
+==== Cellular component to molecular function ====
+* [ftp://ftp.geneontology.org/pub/go/scratch/obol_results/cellular_component_links_to_molecular_function.obo go/scratch/obol_results/cellular_component_links_to_molecular_function.obo]
-this was designed to be a separate editors and for-public version of the ontology. However, the editors version has been advertised as the file to download for the public wishing to get obof1.2 features.
+==== Implementation ====
-One possibility is to migrate to the following:
+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.obo            -- for-public, currently obof1.0, may switch to obof1.2
+       gene_ontology_editorial.obo
-       gene_ontology_edit.obo       -- deprecated, obof1.2
+       function_to_process.obo
-      gene_ontology.obo_1_0        -- for-public, GUARANTEED obof1.0
+       component_to_function.obo
-       gene_ontology.obo_1_2        -- for-public, GUARANTEED obof1.2
-      gene_ontology_editorial.obo  -- for-editors
-This may be done in the context of the [[Versioning_Proposal]]
+===== OBO-Edit =====
-== Ontology linking and cross-products ==
+OBO-Edit is capable of handling these links
-=== Internal (Intra-GO) links ===
+[[Image:hd-complex.jpg]]
-==== Biological process to molecular function ====
+===== AmiGO =====
-==== Cellular component to molecular function ====
+[[AmiGO:Inter-ontology_links]]
 === Internal cross-products ===
@@ Line 42: / Line 60: @@
 ==== Regulation cross-products ====
-[[Regulation_cross_products]]
+[[Regulation_cross-products]]
 ==== Other internal cross-products ====
+* [ftp://ftp.geneontology.org/pub/go/scratch/obol_results/biological_process_xp_cell-obol.obo go/scratch/obol_results/biological_process_xp_cell-obol.obo]
 === 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:
+[http://wiki.geneontology.org/index.php/XP:Meetings]
+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.
+[[Cell cross-products]]
+==== biological_process_xp_chebi ====
+Initial set by mike Bada
+[[Chebi cross-products]]
+Ongoing issues:
+* plurals in ChEBI
+* roles in chebi
+* unusual DAG structure
+==== Others ====
+[http://www.berkeleybop.org/obol Obol]