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.
- adult_mouse_anatomy_xp-obol
- biological_process_xp-obol
- biological_process_xp_anatomy-obol
- biological_process_xp_cell-obol
- biological_process_xp_cellular_component-obol
- biological_process_xp_chebi-obol
- biological_process_xp_development-obol
- biological_process_xp_fly_anatomy-obol
- biological_process_xp_human_anatomy-obol
- biological_process_xp_mouse_anatomy-obol
- biological_process_xp_plant_anatomy-obol
- biological_process_xp_quality-obol
- biological_process_xp_regulation_of_function-obol
- biological_process_xp_regulation_of_process-obol
- biological_process_xp_self-obol
- biological_process_xp_sequence-obol
- biological_process_xp_xenopus_anatomy-obol
- biological_process_xp_zebrafish_anatomy-obol
- cell_xp-obol
- cellular_component_xp_go-obol
- dictyostelium_anatomy_xp-obol
- envo_xp-obol
- fly_anatomy_xp-obol
- fly_anatomy_xp_cell-obol
- fma_xp-obol
- mammalian_phenotype_xp-obol
- molecular_function_xp_chebi-obol
- molecular_function_xp_go-obol
- plant_trait_xp-obol
- po_anatomy_xp-obol
- po_anatomy_xp_cell-obol
- tick_anatomy_xp-obol
- worm_anatomy_xp-obol
- worm_phenotype_xp-obol
- zebrafish_anatomy_xp-obol
- zebrafish_anatomy_xp_cell-obol
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.
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 |
| Browse | Static HTML Summary |
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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 |
| Browse | Static HTML Summary |
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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 |
| Browse | Static HTML Summary |
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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 |
| Browse | Static HTML Summary |
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