Obol

Obol is the name of a piece of software for automatically generating cross-product definitions (aka genus-differentia definitions) from the names of terms/classes in OBO ontologies. It relies on (a) a consistent grammatical style employed in naming terms or exact synonyms (b) Consistent naming across ontologies

Obol generates results in .obo format, which can also be converted to owl. The results are in the form of genus-differentia definitions, which can then be fed into a reasoner to check for consistency between and within ontologies, or can be used for cross-ontology queries

Obol will also generate synonyms for terms, based on the synonyms of the cross-product component terms. It will also (to a lesser extent) generate textual definitions, based on the xp definition, and the standard definition forms used in GO

Page contents

Result Summary

These results are for automated Obol runs - they are unvetted. For vetted/curated cross-products, please see the logical definitions section of the Berkeley OBO Download Matrix.

Grid View

Each row shows an OBO ontology that has been enhanced/extended with cross-products. Each column shows an OBO ontology that is required in some cross-product file. Each cell shows a cross-product file; a file can be repeated across columns, but not across rows - it only "enhances" one OBO ontology. Click on the file for more info.

{requires}
{extends} adult_mouse_anatomy biological_process caro cell cellular_component chebi fly_anatomy fma_lite molecular_function plant_anatomy plant_environment po_anatomy quality relationship ro_proposed ro_ucdhsc sequence worm_anatomy xenopus_anatomy zebrafish_anatomy
adult_mouse_anatomy  adult_mouse_anatomy_xp-obol
                         adult_mouse_anatomy_xp-obol
           
biological_process  biological_process_xp_anatomy-obol
biological_process_xp_mouse_anatomy-obol
 biological_process_xp-obol
biological_process_xp_regulation_of_function-obol
biological_process_xp_regulation_of_process-obol
biological_process_xp_quality-obol
biological_process_xp_cellular_component-obol
biological_process_xp_self-obol
biological_process_xp_cell-obol
biological_process_xp_sequence-obol
biological_process_xp_chebi-obol
biological_process_xp_anatomy-obol
biological_process_xp_development-obol
biological_process_xp_zebrafish_anatomy-obol
biological_process_xp_xenopus_anatomy-obol
biological_process_xp_human_anatomy-obol
biological_process_xp_fly_anatomy-obol
biological_process_xp_plant_anatomy-obol
biological_process_xp_mouse_anatomy-obol
   biological_process_xp-obol
biological_process_xp_quality-obol
biological_process_xp_cell-obol
biological_process_xp_anatomy-obol
biological_process_xp_development-obol
biological_process_xp_zebrafish_anatomy-obol
biological_process_xp_xenopus_anatomy-obol
biological_process_xp_human_anatomy-obol
biological_process_xp_fly_anatomy-obol
biological_process_xp_plant_anatomy-obol
biological_process_xp_mouse_anatomy-obol
 biological_process_xp-obol
biological_process_xp_quality-obol
biological_process_xp_cellular_component-obol
biological_process_xp_cell-obol
biological_process_xp_anatomy-obol
biological_process_xp_development-obol
biological_process_xp_zebrafish_anatomy-obol
biological_process_xp_xenopus_anatomy-obol
biological_process_xp_human_anatomy-obol
biological_process_xp_fly_anatomy-obol
biological_process_xp_plant_anatomy-obol
biological_process_xp_mouse_anatomy-obol
 biological_process_xp-obol
biological_process_xp_quality-obol
biological_process_xp_sequence-obol
biological_process_xp_chebi-obol
 biological_process_xp_anatomy-obol
biological_process_xp_fly_anatomy-obol
 biological_process_xp_human_anatomy-obol
 biological_process_xp-obol
biological_process_xp_regulation_of_function-obol
biological_process_xp_anatomy-obol
 biological_process_xp_anatomy-obol
   biological_process_xp_plant_anatomy-obol
 biological_process_xp-obol
biological_process_xp_quality-obol
biological_process_xp_zebrafish_anatomy-obol
biological_process_xp_xenopus_anatomy-obol
biological_process_xp_human_anatomy-obol
biological_process_xp_fly_anatomy-obol
biological_process_xp_plant_anatomy-obol
biological_process_xp_mouse_anatomy-obol
 biological_process_xp-obol
biological_process_xp_regulation_of_function-obol
biological_process_xp_regulation_of_process-obol
biological_process_xp_quality-obol
biological_process_xp_cellular_component-obol
biological_process_xp_self-obol
biological_process_xp_cell-obol
biological_process_xp_sequence-obol
biological_process_xp_chebi-obol
biological_process_xp_anatomy-obol
biological_process_xp_development-obol
biological_process_xp_zebrafish_anatomy-obol
biological_process_xp_xenopus_anatomy-obol
biological_process_xp_human_anatomy-obol
biological_process_xp_fly_anatomy-obol
biological_process_xp_plant_anatomy-obol
biological_process_xp_mouse_anatomy-obol
 biological_process_xp-obol
biological_process_xp_regulation_of_function-obol
biological_process_xp_regulation_of_process-obol
biological_process_xp_quality-obol
biological_process_xp_cellular_component-obol
biological_process_xp_self-obol
biological_process_xp_cell-obol
biological_process_xp_sequence-obol
biological_process_xp_chebi-obol
biological_process_xp_anatomy-obol
biological_process_xp_development-obol
biological_process_xp_zebrafish_anatomy-obol
biological_process_xp_xenopus_anatomy-obol
biological_process_xp_human_anatomy-obol
biological_process_xp_fly_anatomy-obol
biological_process_xp_plant_anatomy-obol
biological_process_xp_mouse_anatomy-obol
 biological_process_xp-obol
 biological_process_xp_sequence-obol
   biological_process_xp_xenopus_anatomy-obol
 biological_process_xp_anatomy-obol
biological_process_xp_zebrafish_anatomy-obol
cell        cell_xp-obol
 cell_xp-obol
 cell_xp-obol
             cell_xp-obol
 cell_xp-obol
 cell_xp-obol
         
cellular_component    cellular_component_xp_go-obol
   cellular_component_xp_go-obol
 cellular_component_xp_go-obol
       cellular_component_xp_go-obol
         cellular_component_xp_go-obol
 cellular_component_xp_go-obol
         
dictyostelium_discoideum_anatomy                            dictyostelium_anatomy_xp-obol
           
envo            envo_xp-obol
             envo_xp-obol
 envo_xp-obol
 envo_xp-obol
         
fly_anatomy      fly_anatomy_xp-obol
 fly_anatomy_xp_cell-obol
     fly_anatomy_xp-obol
fly_anatomy_xp_cell-obol
             fly_anatomy_xp-obol
fly_anatomy_xp_cell-obol
           
fma_lite                fma_xp-obol
           fma_xp-obol
           
mammalian_phenotype  mammalian_phenotype_xp-obol
 mammalian_phenotype_xp-obol
   mammalian_phenotype_xp-obol
 mammalian_phenotype_xp-obol
       mammalian_phenotype_xp-obol
       mammalian_phenotype_xp-obol
 mammalian_phenotype_xp-obol
 mammalian_phenotype_xp-obol
         
molecular_function    molecular_function_xp_chebi-obol
molecular_function_xp_go-obol
     molecular_function_xp_go-obol
 molecular_function_xp_chebi-obol
     molecular_function_xp_chebi-obol
molecular_function_xp_go-obol
         molecular_function_xp_chebi-obol
molecular_function_xp_go-obol
 molecular_function_xp_chebi-obol
molecular_function_xp_go-obol
         
plant_trait    plant_trait_xp-obol
     plant_trait_xp-obol
       plant_trait_xp-obol
   plant_trait_xp-obol
 plant_trait_xp-obol
 plant_trait_xp-obol
 plant_trait_xp-obol
 plant_trait_xp-obol
         
po_anatomy        po_anatomy_xp_cell-obol
               po_anatomy_xp-obol
po_anatomy_xp_cell-obol
   po_anatomy_xp-obol
po_anatomy_xp_cell-obol
           
tick_anatomy                            tick_anatomy_xp-obol
 tick_anatomy_xp-obol
         
worm_anatomy                            worm_anatomy_xp-obol
 worm_anatomy_xp-obol
     worm_anatomy_xp-obol
   
worm_phenotype    worm_phenotype_xp-obol
   worm_phenotype_xp-obol
 worm_phenotype_xp-obol
 worm_phenotype_xp-obol
     worm_phenotype_xp-obol
       worm_phenotype_xp-obol
 worm_phenotype_xp-obol
 worm_phenotype_xp-obol
     worm_phenotype_xp-obol
   
zebrafish_anatomy        zebrafish_anatomy_xp_cell-obol
                   zebrafish_anatomy_xp-obol
zebrafish_anatomy_xp_cell-obol
           zebrafish_anatomy_xp-obol
zebrafish_anatomy_xp_cell-obol

Details

adult_mouse_anatomy_xp-obol : automated cross products for adult mouse anatomy (internal) (MA)

Description Automated cross-products for Adult Mouse Anatomy (JAX). All internal - no other OBO ontologies used. These logical definitions / cross products have been automatically generated - use with caution!
Source http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/anatomy_xp/adult_mouse_anatomy_xp.obo
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biological_process_xp-obol : automated cross products for GO biological process and various other ontologies

Description Cross-products for GO process terms to other OBO ontologies, and internal cross-products. This set is currently something of a mixed bag. May be redundancies with other xp files below. Eventually this will be generated automatically from biological_process_xp_*.
Source ftp://ftp.geneontology.org/pub/go/scratch/obol_results/biological_process_xp-obol.obo
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biological_process_xp_anatomy-obol : GO biological process cross products to various anatomy ontologies

Description Definitions of GO biological processes (development, morphogenesis) involving anatomical entity terms taken from a mixture of taxon AOs. EXPERIMENTAL!! There is no one single shared AO with deep coverage. Certain entities such as "antenna" are only represented in a single OBO AO. Others, like "gut" are represented in many. In the latter case we just pick one arbitrarily. This makes this file very problematic! Contrast this approach with the de-novo approach (biological_process_xp_development), and with the taxon-specific contextual approaches (biological_process_xp_fly_anatomy, ...) below
Source ftp://ftp.geneontology.org/pub/go/scratch/obol_results/biological_process_xp_anatomy-obol.obo
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biological_process_xp_cell-obol : GO biological process cross products to cell

Description Cross-products for GO process terms to OBO Cell ontology. Automatically generated. Note: currently redundant with go_xp_cell; the two sets will be merged. Examples: neuron differentiation = cell differentiation that results_in_acquisition_of_features_of a neuron. These xps make use of a number of new relations, currently in the ro_proposed holding area. These auto-generated xps are of a reasonably high quality (but have still not been vetted manually).
Source ftp://ftp.geneontology.org/pub/go/scratch/obol_results/biological_process_xp_cell-obol.obo
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biological_process_xp_cellular_component-obol : GO biological process cross products to GO cellular_component (internal xps)

Description Cross-products for GO process terms to GO cellular component terms. Examples: spore wall assembly. These xps are internal to GO - no external OBO ontologies are used. May contain numerous syetmatic errors: eg plasma membrane acetate transport = transport of plasma membrane; to be fixed.
Source ftp://ftp.geneontology.org/pub/go/scratch/obol_results/biological_process_xp_cellular_component-obol.obo
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biological_process_xp_chebi-obol : GO biological process cross products to chebi, additions

Description Additional Cross-products for GO process terms to ChEBI. Automatically generated as an addition to go_xp_chebi
Source ftp://ftp.geneontology.org/pub/go/scratch/obol_results/biological_process_xp_chebi-obol.obo
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biological_process_xp_development-obol : GO biological process cross products to de-novo anatomy ontology

Description The approach taken here is to realize the implicit multi-species anatomical ontology embedded in GO. Highly experimental. For example, the term "brain development" will be used to extract a new term "brain", also used in the definition. These terms are available as "anonymous terms" at the bottom of the file (some of them are further decomposed and defined). This could be the basis of a de-novo multi-species anatomy. It could also be mapped to existing taxon-centric anatomy ontologies. This file provides ALTERNATE xp definitions for those found in the other taxon-centric xp_anatomy files (eg biological_process_xp_zebrafish_anatomy)
Source ftp://ftp.geneontology.org/pub/go/scratch/obol_results/biological_process_xp_development-obol.obo
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biological_process_xp_fly_anatomy-obol : GO biological process cross products to fly anatomy

Description Cross-products for GO process terms to fly_anatomy. We "contextualize" the GO terms to insects. As this is automated there will obviously be some mistakes (particularly w.r.t "eye development" and other non-homologous anatomical entities)
Source ftp://ftp.geneontology.org/pub/go/scratch/obol_results/biological_process_xp_fly_anatomy-obol.obo
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biological_process_xp_human_anatomy-obol : GO biological process cross products to FMA

Description Cross-products for GO process terms to the Foundational Model of Anatomy (FMA) ontology, which contains classes representing adult anatomical entities. We "contextualize" the GO terms to humans.
Source ftp://ftp.geneontology.org/pub/go/scratch/obol_results/biological_process_xp_human_anatomy-obol.obo
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biological_process_xp_mouse_anatomy-obol : GO biological process cross products to PATO

Description Cross-products for GO process terms to MA. We "contextualize" the GO terms to mouse.
Source ftp://ftp.geneontology.org/pub/go/scratch/obol_results/biological_process_xp_mouse_anatomy-obol.obo
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biological_process_xp_plant_anatomy-obol : GO biological process cross products to plant anatomy

Description Cross-products for GO process terms to PO. We "contextualize" the GO terms to plants
Source ftp://ftp.geneontology.org/pub/go/scratch/obol_results/biological_process_xp_plant_anatomy-obol.obo
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biological_process_xp_quality-obol : GO biological process cross products to PATO (using CL and CHEBI)

Description Cross-products for GO process terms to PATO. This is primarily for "regulation of biological quality" terms. At present, this list of xps is rather limited. It includes xp defs that refer to cellular component types, cell types or chemical entity types (for example: *regulation of autophagic vacuole size*, *reduction of cytosolic calcium ion concentration*). However, qualities of gross anatomical entities (eg *regulation of /blood/ pressure*) are found in the biological_process_xp_*TAXON*_anatomy xp files, not here.
Source ftp://ftp.geneontology.org/pub/go/scratch/obol_results/biological_process_xp_quality-obol.obo
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biological_process_xp_regulation_of_function-obol : GO biological process cross products to molecular function regulation terms

Description Cross-products for GO biological process terms that are kinds of regulation of molecular function. See also regulation_of_biological_process and regulation_of_quality
Source ftp://ftp.geneontology.org/pub/go/scratch/obol_results/biological_process_xp_regulation_of_function-obol.obo
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biological_process_xp_regulation_of_process-obol : GO biological process cross products to molecular process regulation terms

Description Cross-products for GO biological process terms that are kinds of regulation of biological process. This is exactly the same as the "vetted" file available from the main OBO Downloads page (http://www.berkeleybop.org/ontologies#go_xp_regulation) but is included here for completeness, to mirror the other regulation xps
Source ftp://ftp.geneontology.org/pub/go/scratch/obol_results/biological_process_xp_regulation_of_process-obol.obo
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biological_process_xp_self-obol : GO biological process cross products to BP (internal xps)

Description Cross-products for GO biological process terms to other GO biological process terms, excluding those found in biological_process_xp_regulation_of_process. Examples: tolerance induction dependent upon immune response.. These xps are internal to GO - no external OBO ontologies are used.
Source ftp://ftp.geneontology.org/pub/go/scratch/obol_results/biological_process_xp_self-obol.obo
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biological_process_xp_sequence-obol : GO biological process cross products to sequence bearing molecules (SO)

Description EXPERIMENTAL. Cross-products for GO process terms to SO. This involves treating SO terms as if they represented molecular entities, rather than the sequences of these entities. This results in some definition clashes with existing xp files (for example, "chromosome localization" is already defined in biological_process_xp_cellular_component); these are mostly excluded.
Source ftp://ftp.geneontology.org/pub/go/scratch/obol_results/biological_process_xp_sequence-obol.obo
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biological_process_xp_xenopus_anatomy-obol : GO biological process cross products to xenopus anatomy

Description Cross-products for GO process terms to the Xenopus (frog) anatomy ontology. We "contextualize" the GO terms to frogs.
Source ftp://ftp.geneontology.org/pub/go/scratch/obol_results/biological_process_xp_xenopus_anatomy-obol.obo
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