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 |
| Browse | Static HTML Summary |
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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 |
| Browse | Static HTML Summary |
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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 |
| Browse | Static HTML Summary |
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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 |
| Browse | Static HTML Summary |
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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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biological_process_xp_zebrafish_anatomy-obol : GO biological process cross products to zebrafish anatomy
| Description | Cross-products for GO process terms to ZFA. We "contextualize" the GO terms to ZFA |
| Source | ftp://ftp.geneontology.org/pub/go/scratch/obol_results/biological_process_xp_zebrafish_anatomy-obol.obo |
| Browse | Static HTML Summary |
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cell_xp-obol : Cell cross products to GO, PATO and CHEBI
| Description | Automated cross-products for OBO Cell ontology, referencing GO and PATO. Examples: estradiol secreting cell = cell that outputs estradiol; anucleate cell = cell that lacks_part nucleus Some of these are a little dodgy. Eg: contractile cell = cell that has_quality contractile - this is not a good definition |
| Source | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/anatomy_xp/cell_xp.obo |
| Browse | Static HTML Summary |
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cellular_component_xp_go-obol : GO cellular component cross products within GO
| Description | Cross-products for GO cellular component terms to other GO terms. Examples: Golgi membrane = membrane that is part_of Golgi apparatus; voltage-gated sodium channel complex |
| Source | ftp://ftp.geneontology.org/pub/go/scratch/obol_results/cellular_component_xp_go-obol.obo |
| Browse | Static HTML Summary |
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dictyostelium_anatomy_xp-obol : automated cross products for dictyostelium anatomy (internal)
| Description | Automated cross-products for dictyostelium discoideum anatomy. All internal - no other OBO ontologies used. These logical definitions / cross products have been automatically generated - use with caution! Obol creates terms on-the-fly (anonymous classes) such as "surface sheath" and "mound" in order to create defs for "surface sheath of the mound" |
| Source | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/anatomy_xp/dictyostelium_anatomy_xp.obo |
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envo_xp-obol : Environment ontology cross-products
| Description | Cross-products for Environment Ontology. Examples: arsenic-rich mud |
| Source | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/phenotype_xp/envo_xp-obol.obo |
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fly_anatomy_xp-obol : automated cross products for fly anatomy (mostly internal)
| Description | Automated cross-products for fly anatomy. 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/fly_anatomy_xp.obo |
| Browse | Static HTML Summary |
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fly_anatomy_xp_cell-obol : promoted cross products for fly anatomy to OBO cell ontology
| Description | Promoted xrefs; any FB term with an xref to a CL ID is treated as the fly-specific subtype of that cell. We use taxid 7277 (D mel). |
| Source | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/anatomy_xp/fly_anatomy_xp_cell.obo |
| Browse | Static HTML Summary |
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fma_xp-obol : automated cross products for FMA-lite
| Description | Automated cross-products for Foundational Model of Anatomy (lite version). All internal - no other OBO ontologies used. These logical definitions / cross products have been automatically generated - use with caution! Examples of generated xp defs: parotid duct = duct that part_of parotid gland |
| Source | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/anatomy_xp/fma_xp.obo |
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mammalian_phenotype_xp-obol : MP cross products, additions
| Description | Additional cross-products for MP, generated automatically by Obol. Extends the curated set, mammalian_phenotype_xp. This automated export is occasionally vetted and imported into the curated set |
| Source | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/phenotype_xp/mammalian_phenotype_xp-obol.obo |
| Browse | Static HTML Summary |
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molecular_function_xp_chebi-obol : GO molecular function cross products to chebi
| Description | Cross-products for GO function terms to ChEBI. Highly incomplete |
| Source | ftp://ftp.geneontology.org/pub/go/scratch/obol_results/molecular_function_xp_chebi-obol.obo |
| Browse | Static HTML Summary |
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molecular_function_xp_go-obol : GO molecular function cross products to the rest of GO
| Description | Cross-products for GO function terms to rest of GO. Current just structural constituent terms, eg "structural constituent of cell wall". Also a few like "microtubule motor activity" |
| Source | ftp://ftp.geneontology.org/pub/go/scratch/obol_results/molecular_function_xp_go-obol.obo |
| Browse | Static HTML Summary |
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plant_trait_xp-obol : plant_trait cross products, additions
| Description | Additional cross-products for TO, generated automatically by Obol. Extends the curated set, plant_trait_xp. |
| Source | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/phenotype_xp/plant_trait_xp-obol.obo |
| Browse | Static HTML Summary |
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po_anatomy_xp-obol : automated cross products for plant anatomy (internal)
| Description | Automated cross-products for plant anatomy (internal). 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/po_anatomy_xp.obo |
| Browse | Static HTML Summary |
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po_anatomy_xp_cell-obol : promoted cross products for plant anatomy to OBO cell ontology
| Description | Promoted xrefs; any PO term with an xref to a CL ID is treated as the plant-specific subtype of that cell. We use taxid 33090 Viridiplantae. Examples: PO:egg_cell is_a CL:egg_cell that part_of some plant. See http://www.bioontology.org/wiki/index.php/CL:Aligning_species-specific_anatomy_ontologies_with_CL |
| Source | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/anatomy_xp/plant_anatomy_xp_cell.obo |
| Browse | Static HTML Summary |
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tick_anatomy_xp-obol : automated cross products for tick anatomy (internal)
| Description | Automated cross-products for tick anatomy. All internal - no other OBO ontologies used. These logical definitions / cross products have been automatically generated - use with caution! Example: Adult midgut lumen = anatomical space that surrounded_by adult midgut |
| Source | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/anatomy_xp/tick_anatomy_xp.obo |
| Browse | Static HTML Summary |
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worm_anatomy_xp-obol : automated cross products for worm anatomy (internal)
| Description | Automated cross-products for worm anatomy. 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/worm_anatomy_xp.obo |
| Browse | Static HTML Summary |
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worm_phenotype_xp-obol : MP cross products, additions
| Description | Cross-products for worm_phenotype, generated automatically by Obol. As a result of the automatic generation process, suggestions are made for new GO terms to help complete the definitions. E.g. for "necrotic cell death increased" obol creates an on-the-fly process term "necrotic cell death", and attempts to create ab xp def for this term. Most of these should be ignored. |
| Source | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/phenotype_xp/worm_phenotype_xp-obol.obo |
| Browse | Static HTML Summary |
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zebrafish_anatomy_xp-obol : automated cross products for zebrafish anatomy (internal)
| Description | Automated cross-products for plant anatomy. 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/zebrafish_anatomy_xp.obo |
| Browse | Static HTML Summary |
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zebrafish_anatomy_xp_cell-obol : promoted cross products for zebrafish anatomy to OBO cell ontology
| Description | Promoted xrefs; any ZFA term with an xref to a CL ID is treated as the fish-specific subtype of that cell. We use taxid 7955 (D rerio), but it could be more general (teleost? Cypriniforme?). Examples: ZF:erythrocyte is_a CL:nucleate_erythrocyte that part_of some teleost organism. See http://www.bioontology.org/wiki/index.php/CL:Aligning_species-specific_anatomy_ontologies_with_CL |
| Source | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/anatomy_xp/zebrafish_anatomy_xp_cell.obo |
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Using the results
Obol produces genus-differentia definitions using the .obo intersection_of tag. For example, the term oocyte growth would be parsed to the following:
[Term]
id: GO:0001555 ! oocyte growth
intersection_of: GO:0040007 ! growth
intersection_of: OBO_REL:results_in_increase_in_mass_of CL:0000023 ! oocyte
This can be read as:
oocyte growth is a growth that results_in_increase_in_mass_of an oocyte
You can browse the .obo files directly, or load them into
oboedit. If you do this, it is recommended you load the
.imports.obo file - this has processing instructions
for loading all the dependent cross-product ontologies
You can also use an OWL client, such as Protege or SWOOP. In this case, load the .owl file. Again, you will probably want to use the .imports.owl file
Formats
The following formats are generated. See below for caveats. All indexed ontologies can be downloaded en-masse for any one particular format, see download section below. The format metadata spec can be found Here
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obo-- The Obo text format. If this is not the source format, this is generated using flat2obo (part of obo-edit)
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obo_xml-- The Obo XML format. Generated using go-perl
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owl-- See W3 OWL page for details. Generated from obo-xml using oboxml_to_owl.xsl. See OboInOwl for details of mapping. All obo files converted to owl are made available using the http://purl.org/obo/ URI scheme; for example http://purl.org/obo/GO
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chadoxml-- See Chado-XML pages. This format can be loaded into a Chado-schema database using a generic loader such as DBStag.
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prolog-- Prolog database. Can be reasoned over using a prolog engine. See obol and blip.
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owl-classified-by-pellet-- result of running the OWL through the peller classifier. Potentially includes missing subclasses
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obo-classified-by-oboedit-- result of running the obo through the oboedit reasoner. Potentially includes missing is_a and relationship links. For best results, see the logical definitions files.
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obo-classified-by-blip-- missing subclasses and explanations of why they should be added
Presentations, articles and Papers
Obol: integrating language and meaning in bio-ontologies
Appears in: Comparative and Functional Genomics; Volume 5, Issue 6-7, 2004. Pages 509-520
- Format: [ PDF ]
This is a fairly CS-oriented discussion of the theory behind Obol. The paper also includes the initial Obol results.
Managing complexity in the GO
NOTE: the powerpoint that was previously posted here (prior to 2005/10/22) had lots of missing slides - the correct version is below
This presentation outlines the rationale for Obol by examining both the rise in complexity in GO and inconsistencies between the OBO cell type ontology and the implicit cell type ontology in GO
- Format: [ PowerPoint | PDF ]
Obol at Bio-Ontologies 2004
This presentation covers the theory behind how Obol works and presents some initial results, fleshed out in more detail in the paper below
- Format: [ PowerPoint | PDF ]
Articles
Your database is talking. Is anyone listening? This article, which appeared in The Scientist, mentions Obol.