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COMMITTEE
The Open Biological and Biomedical Ontology (OBO) Foundry Community development of interoperable ontologies for the biological sciences Learn about OBO best practices and community resourcesCELL ONTOLOGY
OntoBee AberOWL OLS. The Cell Ontology is designed as a structured controlled vocabulary for cell types. This ontology was constructed for use by the model organism and other bioinformatics databases, where there is a need for a controlled vocabulary of cell types.PLANT ONTOLOGY
Plant Ontology The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. INFORMATION ARTIFACT ONTOLOGY An ontology of information entities. OntoBee AberOWL OLS. The Information Artifact Ontology (IAO) is a new ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch. MONDO DISEASE ONTOLOGY OntoBee AberOWL OLS Monarch. The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world. It is a semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology.DATA USE ONTOLOGY
DUO is an ontology which represent data use conditions. Data Use Ontology DUO is an ontology which represent data use conditions. PROTEIN ONTOLOGY (PRO) An ontological representation of protein-related entities. OntoBee AberOWL OLS BioPortal PRO. The PRotein Ontology (PRO) formally defines taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins producedTHE DRUG ONTOLOGY
OntoBee AberOWL OLS. We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive). CHEMICAL INFORMATION ONTOLOGY Chemical Information Ontology Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them. MENTAL DISEASE ONTOLOGY OntoBee AberOWL OLS. An ontology to describe and classify mental diseases such as schizophrenia, annotated with DSM-IV and ICD codes where applicable. Historic note: The IDs used in this ontology all have the MFOMD, as this ontology was originally conceived as part of mf, but the official title for this ontology is the “Mental DiseaseOntology”
THE OBO FOUNDRYABOUTPRINCIPLESONTOLOGIESRESOURCESCITATIONOPERATIONSCOMMITTEE
The Open Biological and Biomedical Ontology (OBO) Foundry Community development of interoperable ontologies for the biological sciences Learn about OBO best practices and community resourcesCELL ONTOLOGY
OntoBee AberOWL OLS. The Cell Ontology is designed as a structured controlled vocabulary for cell types. This ontology was constructed for use by the model organism and other bioinformatics databases, where there is a need for a controlled vocabulary of cell types.PLANT ONTOLOGY
Plant Ontology The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. INFORMATION ARTIFACT ONTOLOGY An ontology of information entities. OntoBee AberOWL OLS. The Information Artifact Ontology (IAO) is a new ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch. MONDO DISEASE ONTOLOGY OntoBee AberOWL OLS Monarch. The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world. It is a semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology.DATA USE ONTOLOGY
DUO is an ontology which represent data use conditions. Data Use Ontology DUO is an ontology which represent data use conditions. PROTEIN ONTOLOGY (PRO) An ontological representation of protein-related entities. OntoBee AberOWL OLS BioPortal PRO. The PRotein Ontology (PRO) formally defines taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins producedTHE DRUG ONTOLOGY
OntoBee AberOWL OLS. We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive). CHEMICAL INFORMATION ONTOLOGY Chemical Information Ontology Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them. MENTAL DISEASE ONTOLOGY OntoBee AberOWL OLS. An ontology to describe and classify mental diseases such as schizophrenia, annotated with DSM-IV and ICD codes where applicable. Historic note: The IDs used in this ontology all have the MFOMD, as this ontology was originally conceived as part of mf, but the official title for this ontology is the “Mental DiseaseOntology”
RESOURCES - OBO) FOUNDRY Ontology Tools and Resources Ontology Browsers. OBO Foundry; BioPortal; Ontology Lookup Service; Ontobee; QuickGO; AmiGO; Linked Open Vocabularies; Tutorials. Introduction to Ontologies: slides from Cold Spring Harbor workshop, October 2018, by Nicole Vasilevsky.; Ontology 101 Tutorial: from International Conference on Biological Ontology (ICBO) 2018; Ontology 101 Open Educational BIOLOGICAL COLLECTIONS ONTOLOGY OntoBee AberOWL OLS. The Biological Collections Ontology (BCO) is a being developed as an application ontology as part of the Biocode Commons project, within the OBO Foundry framework.PLANT ONTOLOGY
Plant Ontology The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.SYMPTOM ONTOLOGY
OntoBee AberOWL OLS. The symptom ontology was designed around the guiding concept of a symptom being: “A perceived change in function, sensation or appearance reported ANATOMICAL ENTITY ONTOLOGY OntoBee AberOWL OLS. The AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology, to about 160 classes using the is_a relationship; it thus provides a detailed type classification for tissues. MENTAL FUNCTIONING ONTOLOGY OntoBee AberOWL OLS. The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning, founded on the Basic Formal Ontology (BFO) and related to the Ontology for General MedicalScience (OGMS).
MOUSE DEVELOPMENTAL ANATOMY ONTOLOGY OntoBee AberOWL OLS BACKGROUND. The ontology of mouse developmental anatomy was originally developed by Jonathan Bard and his colleagues as part of the Edinburgh Mouse Atlas Project (EMAP) in order to provide a structured controlled vocabulary of stage-specific anatomical structures for the developing laboratory mouse. UNITS OF MEASUREMENT ONTOLOGY Metrical units for use in conjunction with PATO. Units of measurement ontology Metrical units for use in conjunction with PATO NCBI ORGANISMAL CLASSIFICATION OntoBee AberOWL OLS NCBI. The NCBITaxon ontology is an automatic translation of the NCBI taxonomy database into obo/owl.. The translation treats each taxon as an obo/owl class whose instances (for most branches of the ontology) would be individual organisms. WHERE IS THE OBO FILE FOR MY ONTOLOGY? This registry makes a distinction between an ontology and the products (also known as editions) of that ontology.. Products can be the ontology in a different format (e.g. obo vs owl), or they can be different variants (for example, subsets or extensions). THE OBO FOUNDRYABOUTPRINCIPLESONTOLOGIESRESOURCESCITATIONOPERATIONSCOMMITTEE
The Open Biological and Biomedical Ontology (OBO) Foundry Community development of interoperable ontologies for the biological sciences Learn about OBO best practices and community resourcesCELL ONTOLOGY
OntoBee AberOWL OLS. The Cell Ontology is designed as a structured controlled vocabulary for cell types. This ontology was constructed for use by the model organism and other bioinformatics databases, where there is a need for a controlled vocabulary of cell types.PLANT ONTOLOGY
The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. The PO is under active development to expand to encompass terms and annotations from all plants. MONDO DISEASE ONTOLOGY OntoBee AberOWL OLS Monarch. The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world. It is a semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology.DATA USE ONTOLOGY
Data Use Ontology. DUO allows to semantically tag datasets with restriction about their usage, making them discoverable automatically based on the authorization level of users, or intended usage. Human subjects datasets often have restrictions such as “only available for cancer use” or “only available for the study of pediatricdiseases
MENTAL DISEASE ONTOLOGY An ontology to describe and classify mental diseases such as schizophrenia, annotated with DSM-IV and ICD codes where applicable. Historic note: The IDs used in this ontology all have the MFOMD, as this ontology was originally conceived as part of mf, but the official title for this ontology is the “Mental Disease Ontology”. INFORMATION ARTIFACT ONTOLOGY An ontology of information entities. OntoBee AberOWL OLS. The Information Artifact Ontology (IAO) is a new ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch.SYMPTOM ONTOLOGY
Symptom Ontology. An ontology of disease symptoms, with symptoms encompasing perceived changes in function, sensations or appearance reported by a patient indicative of a disease. The symptom ontology was designed around the guiding concept of a symptom being: “A perceived change in function, sensation or appearance reported by apatient
CHEMICAL INFORMATION ONTOLOGY Chemical Information Ontology Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them. PROTEIN ONTOLOGY (PRO) An ontological representation of protein-related entities. OntoBee AberOWL OLS BioPortal PRO. The PRotein Ontology (PRO) formally defines taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced THE OBO FOUNDRYABOUTPRINCIPLESONTOLOGIESRESOURCESCITATIONOPERATIONSCOMMITTEE
The Open Biological and Biomedical Ontology (OBO) Foundry Community development of interoperable ontologies for the biological sciences Learn about OBO best practices and community resourcesCELL ONTOLOGY
OntoBee AberOWL OLS. The Cell Ontology is designed as a structured controlled vocabulary for cell types. This ontology was constructed for use by the model organism and other bioinformatics databases, where there is a need for a controlled vocabulary of cell types.PLANT ONTOLOGY
The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. The PO is under active development to expand to encompass terms and annotations from all plants. MONDO DISEASE ONTOLOGY OntoBee AberOWL OLS Monarch. The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world. It is a semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology.DATA USE ONTOLOGY
Data Use Ontology. DUO allows to semantically tag datasets with restriction about their usage, making them discoverable automatically based on the authorization level of users, or intended usage. Human subjects datasets often have restrictions such as “only available for cancer use” or “only available for the study of pediatricdiseases
MENTAL DISEASE ONTOLOGY An ontology to describe and classify mental diseases such as schizophrenia, annotated with DSM-IV and ICD codes where applicable. Historic note: The IDs used in this ontology all have the MFOMD, as this ontology was originally conceived as part of mf, but the official title for this ontology is the “Mental Disease Ontology”. INFORMATION ARTIFACT ONTOLOGY An ontology of information entities. OntoBee AberOWL OLS. The Information Artifact Ontology (IAO) is a new ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch.SYMPTOM ONTOLOGY
Symptom Ontology. An ontology of disease symptoms, with symptoms encompasing perceived changes in function, sensations or appearance reported by a patient indicative of a disease. The symptom ontology was designed around the guiding concept of a symptom being: “A perceived change in function, sensation or appearance reported by apatient
CHEMICAL INFORMATION ONTOLOGY Chemical Information Ontology Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them. PROTEIN ONTOLOGY (PRO) An ontological representation of protein-related entities. OntoBee AberOWL OLS BioPortal PRO. The PRotein Ontology (PRO) formally defines taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced RESOURCES - OBO) FOUNDRY Ontology Development Kit: A toolkit to initialize an OBO library repository and associated files. ROBOT: ROBOT is a tool for working with Open Biomedical Ontologies. VOCOL: An Integrated Environment for Collaborative Vocabulary Development. Karma Data Integration: A data integration tool. Ontofox: An ontology term and relation extractionand
PLANT ONTOLOGY
The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. The PO is under active development to expand to encompass terms and annotations from all plants. BIOLOGICAL COLLECTIONS ONTOLOGY OntoBee AberOWL OLS. The Biological Collections Ontology (BCO) is a being developed as an application ontology as part of the Biocode Commons project, within the OBO Foundry framework.GENE ONTOLOGY
Gene Ontology. An ontology for describing the function of genes and gene products. The goal of the GeneOntology (GO) project is to provide a uniformway to describe the functions of gene products from organisms across all kingdoms of life and thereby enable analysis of genomicdata.
MENTAL FUNCTIONING ONTOLOGY The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning. The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning, founded on the Basic Formal Ontology (BFO) and related to the Ontology for General Medical Science (OGMS).SYMPTOM ONTOLOGY
Symptom Ontology. An ontology of disease symptoms, with symptoms encompasing perceived changes in function, sensations or appearance reported by a patient indicative of a disease. The symptom ontology was designed around the guiding concept of a symptom being: “A perceived change in function, sensation or appearance reported by apatient
ANATOMICAL ENTITY ONTOLOGY OntoBee AberOWL OLS. The AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology, to about 160 classes using the is_a relationship; it thus provides a detailed type classification for tissues. NCBI ORGANISMAL CLASSIFICATION NCBI organismal classification. An ontology representation of the NCBI organismal taxonomy. This ontology uses a mixed-case prefix. Identifiers and URIs should use "NCBITaxon". The NCBITaxon ontology is an automatic translation of the NCBI taxonomy database into obo/owl. The translation treats each taxon as an obo/owl class whose instances(for
MOUSE DEVELOPMENTAL ANATOMY ONTOLOGY OntoBee AberOWL OLS BACKGROUND. The ontology of mouse developmental anatomy was originally developed by Jonathan Bard and his colleagues as part of the Edinburgh Mouse Atlas Project (EMAP) in order to provide a structured controlled vocabulary of stage-specific anatomical structures for the developing laboratory mouse. WHERE IS THE OBO FILE FOR MY ONTOLOGY? Ontologies can OPTIONALLY produce an OBO-Format file. This is conventionally the same IRI as the owl, but with .owl changed to .obo. Note that an obo product is not listed by default. If you produce an obo product, you should register it under the products field, as in the file above. It does not matter to us if you maintain the sourcefor your
THE OBO FOUNDRYABOUTPRINCIPLESONTOLOGIESRESOURCESCITATIONOPERATIONSCOMMITTEE
The Open Biological and Biomedical Ontology (OBO) Foundry Community development of interoperable ontologies for the biological sciences Learn about OBO best practices and community resourcesCELL ONTOLOGY
OntoBee AberOWL OLS. The Cell Ontology is designed as a structured controlled vocabulary for cell types. This ontology was constructed for use by the model organism and other bioinformatics databases, where there is a need for a controlled vocabulary of cell types. MONDO DISEASE ONTOLOGY OntoBee AberOWL OLS Monarch. The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world. It is a semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology. MENTAL FUNCTIONING ONTOLOGY The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning. The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning, founded on the Basic Formal Ontology (BFO) and related to the Ontology for General Medical Science (OGMS). BIOLOGICAL COLLECTIONS ONTOLOGY OntoBee AberOWL OLS. The Biological Collections Ontology (BCO) is a being developed as an application ontology as part of the Biocode Commons project, within the OBO Foundry framework.PLANT ONTOLOGY
The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. The PO is under active development to expand to encompass terms and annotations from all plants.DATA USE ONTOLOGY
Data Use Ontology. DUO allows to semantically tag datasets with restriction about their usage, making them discoverable automatically based on the authorization level of users, or intended usage. Human subjects datasets often have restrictions such as “only available for cancer use” or “only available for the study of pediatricdiseases
CHEMICAL INFORMATION ONTOLOGY Chemical Information Ontology Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them. PROTEIN ONTOLOGY (PRO) An ontological representation of protein-related entities. OntoBee AberOWL OLS BioPortal PRO. The PRotein Ontology (PRO) formally defines taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced PRINCIPLE: URI/IDENTIFIER SPACE (PRINCIPLE 3) Details. Each class and relation (property) in the ontology must have a unique URI identifier. The URI should be constructed from a base URI, a prefix that is unique within the Foundry (e.g. GO, CHEBI, CL) and a local identifier (e.g. 0000001). The local identifier should not consist of labels or mnemonics meaningful to humans. THE OBO FOUNDRYABOUTPRINCIPLESONTOLOGIESRESOURCESCITATIONOPERATIONSCOMMITTEE
The Open Biological and Biomedical Ontology (OBO) Foundry Community development of interoperable ontologies for the biological sciences Learn about OBO best practices and community resourcesCELL ONTOLOGY
OntoBee AberOWL OLS. The Cell Ontology is designed as a structured controlled vocabulary for cell types. This ontology was constructed for use by the model organism and other bioinformatics databases, where there is a need for a controlled vocabulary of cell types. MONDO DISEASE ONTOLOGY OntoBee AberOWL OLS Monarch. The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world. It is a semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology. MENTAL FUNCTIONING ONTOLOGY The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning. The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning, founded on the Basic Formal Ontology (BFO) and related to the Ontology for General Medical Science (OGMS). BIOLOGICAL COLLECTIONS ONTOLOGY OntoBee AberOWL OLS. The Biological Collections Ontology (BCO) is a being developed as an application ontology as part of the Biocode Commons project, within the OBO Foundry framework.PLANT ONTOLOGY
The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. The PO is under active development to expand to encompass terms and annotations from all plants.DATA USE ONTOLOGY
Data Use Ontology. DUO allows to semantically tag datasets with restriction about their usage, making them discoverable automatically based on the authorization level of users, or intended usage. Human subjects datasets often have restrictions such as “only available for cancer use” or “only available for the study of pediatricdiseases
CHEMICAL INFORMATION ONTOLOGY Chemical Information Ontology Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them. PROTEIN ONTOLOGY (PRO) An ontological representation of protein-related entities. OntoBee AberOWL OLS BioPortal PRO. The PRotein Ontology (PRO) formally defines taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced PRINCIPLE: URI/IDENTIFIER SPACE (PRINCIPLE 3) Details. Each class and relation (property) in the ontology must have a unique URI identifier. The URI should be constructed from a base URI, a prefix that is unique within the Foundry (e.g. GO, CHEBI, CL) and a local identifier (e.g. 0000001). The local identifier should not consist of labels or mnemonics meaningful to humans. RESOURCES - OBO) FOUNDRY Ontology Development Kit: A toolkit to initialize an OBO library repository and associated files. ROBOT: ROBOT is a tool for working with Open Biomedical Ontologies. VOCOL: An Integrated Environment for Collaborative Vocabulary Development. Karma Data Integration: A data integration tool. Ontofox: An ontology term and relation extractionand
BIOLOGICAL COLLECTIONS ONTOLOGY OntoBee AberOWL OLS. The Biological Collections Ontology (BCO) is a being developed as an application ontology as part of the Biocode Commons project, within the OBO Foundry framework.GENE ONTOLOGY
Gene Ontology. An ontology for describing the function of genes and gene products. The goal of the GeneOntology (GO) project is to provide a uniformway to describe the functions of gene products from organisms across all kingdoms of life and thereby enable analysis of genomicdata.
SOFTWARE ONTOLOGY
The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community. HUMAN PHENOTYPE ONTOLOGY The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM. ANTIBIOTIC RESISTANCE ONTOLOGY Antibiotic Resistance Ontology. The Antibiotic Resistance Ontology describes antibiotic resistance genes and mutations, their products, mechanisms, and associated phenotypes, as well as antibiotics and their molecular targets. It is integrated with the Comprehensive Antibiotic Resistance Database , a curated resource containing highquality
CHEMICAL ENTITIES OF BIOLOGICAL INTEREST Chemical Entities of Biological Interest. A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds. A freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The term ‘molecular entity’ refers to any constitutionally or isotopicallydistinct atom
ANATOMICAL ENTITY ONTOLOGY OntoBee AberOWL OLS. The AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology, to about 160 classes using the is_a relationship; it thus provides a detailed type classification for tissues. NCBI ORGANISMAL CLASSIFICATION NCBI organismal classification. An ontology representation of the NCBI organismal taxonomy. This ontology uses a mixed-case prefix. Identifiers and URIs should use "NCBITaxon". The NCBITaxon ontology is an automatic translation of the NCBI taxonomy database into obo/owl. The translation treats each taxon as an obo/owl class whose instances(for
PRINCIPLE: URI/IDENTIFIER SPACE (PRINCIPLE 3) Details. Each class and relation (property) in the ontology must have a unique URI identifier. The URI should be constructed from a base URI, a prefix that is unique within the Foundry (e.g. GO, CHEBI, CL) and a local identifier (e.g. 0000001). The local identifier should not consist of labels or mnemonics meaningful to humans. THE OBO FOUNDRYABOUTPRINCIPLESONTOLOGIESRESOURCESCITATIONOPERATIONSCOMMITTEE
The Open Biological and Biomedical Ontology (OBO) Foundry Community development of interoperable ontologies for the biological sciences Learn about OBO best practices and community resources RESOURCES - OBO) FOUNDRYOBO FOUNDRYBIOPORTALONTOLOGY LOOKUP SERVICEONTOBEESEE MORE ON OBOFOUNDRY.ORG BIOLOGICAL COLLECTIONS ONTOLOGY OntoBee AberOWL OLS. The Biological Collections Ontology (BCO) is a being developed as an application ontology as part of the Biocode Commons project, within the OBO Foundry framework.CELL ONTOLOGY
OntoBee AberOWL OLS. The Cell Ontology is designed as a structured controlled vocabulary for cell types. This ontology was constructed for use by the model organism and other bioinformatics databases, where there is a need for a controlled vocabulary of cell types.THE DRUG ONTOLOGY
The Drug Ontology. An ontology to support comparative effectiveness researchers studying claims data. We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade),physiological
SOFTWARE ONTOLOGY
The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community.DATA USE ONTOLOGY
Data Use Ontology. DUO allows to semantically tag datasets with restriction about their usage, making them discoverable automatically based on the authorization level of users, or intended usage. Human subjects datasets often have restrictions such as “only available for cancer use” or “only available for the study of pediatricdiseases
PHENOTYPE AND TRAIT ONTOLOGY Phenotype And Trait Ontology. An ontology of phenotypic qualities (properties, attributes or characteristics) Phenotypic qualities (properties). This ontology can be used in conjunction with other ontologies such as GO or anatomical ontologies to refer to phenotypes. Examples of qualities are red, ectopic, high temperature, fused, small INFORMATION ARTIFACT ONTOLOGY An ontology of information entities. OntoBee AberOWL OLS. The Information Artifact Ontology (IAO) is a new ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch. PRINCIPLE: URI/IDENTIFIER SPACE (PRINCIPLE 3) Details. Each class and relation (property) in the ontology must have a unique URI identifier. The URI should be constructed from a base URI, a prefix that is unique within the Foundry (e.g. GO, CHEBI, CL) and a local identifier (e.g. 0000001). The local identifier should not consist of labels or mnemonics meaningful to humans. THE OBO FOUNDRYABOUTPRINCIPLESONTOLOGIESRESOURCESCITATIONOPERATIONSCOMMITTEE
The Open Biological and Biomedical Ontology (OBO) Foundry Community development of interoperable ontologies for the biological sciences Learn about OBO best practices and community resources RESOURCES - OBO) FOUNDRYOBO FOUNDRYBIOPORTALONTOLOGY LOOKUP SERVICEONTOBEESEE MORE ON OBOFOUNDRY.ORG BIOLOGICAL COLLECTIONS ONTOLOGY OntoBee AberOWL OLS. The Biological Collections Ontology (BCO) is a being developed as an application ontology as part of the Biocode Commons project, within the OBO Foundry framework.CELL ONTOLOGY
OntoBee AberOWL OLS. The Cell Ontology is designed as a structured controlled vocabulary for cell types. This ontology was constructed for use by the model organism and other bioinformatics databases, where there is a need for a controlled vocabulary of cell types.THE DRUG ONTOLOGY
The Drug Ontology. An ontology to support comparative effectiveness researchers studying claims data. We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade),physiological
SOFTWARE ONTOLOGY
The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community.DATA USE ONTOLOGY
Data Use Ontology. DUO allows to semantically tag datasets with restriction about their usage, making them discoverable automatically based on the authorization level of users, or intended usage. Human subjects datasets often have restrictions such as “only available for cancer use” or “only available for the study of pediatricdiseases
PHENOTYPE AND TRAIT ONTOLOGY Phenotype And Trait Ontology. An ontology of phenotypic qualities (properties, attributes or characteristics) Phenotypic qualities (properties). This ontology can be used in conjunction with other ontologies such as GO or anatomical ontologies to refer to phenotypes. Examples of qualities are red, ectopic, high temperature, fused, small INFORMATION ARTIFACT ONTOLOGY An ontology of information entities. OntoBee AberOWL OLS. The Information Artifact Ontology (IAO) is a new ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch. PRINCIPLE: URI/IDENTIFIER SPACE (PRINCIPLE 3) Details. Each class and relation (property) in the ontology must have a unique URI identifier. The URI should be constructed from a base URI, a prefix that is unique within the Foundry (e.g. GO, CHEBI, CL) and a local identifier (e.g. 0000001). The local identifier should not consist of labels or mnemonics meaningful to humans. RESOURCES - OBO) FOUNDRY Ontology Development Kit: A toolkit to initialize an OBO library repository and associated files. ROBOT: ROBOT is a tool for working with Open Biomedical Ontologies. VOCOL: An Integrated Environment for Collaborative Vocabulary Development. Karma Data Integration: A data integration tool. Ontofox: An ontology term and relation extractionand
MEMBERSHIP - THE OBO FOUNDRY Current members of the OBO Foundry Operations Committee are (in alphabetical order of surname): Jim Balhoff (T), RENCI, University of North Carolina, Chapel Hill, NC, USA. Mathias Brochhausen (O), University of Arkansas for Medical Sciences, Little Rock, AR, USA. Matt Brush (T), OHSU. MONDO DISEASE ONTOLOGY OntoBee AberOWL OLS Monarch. The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world. It is a semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology.GENE ONTOLOGY
Gene Ontology. An ontology for describing the function of genes and gene products. The goal of the GeneOntology (GO) project is to provide a uniformway to describe the functions of gene products from organisms across all kingdoms of life and thereby enable analysis of genomicdata.
OPERATIONS COMMITTEE Members of the OBO Foundry Operations Committee aim at improving flow of operations and making things happen within the OBO Foundry.Such operations include, but are not limited to, establishment of policies, review of resources, outreach and education. The Editorial Working Group is involved in reviewing OBO Foundry ontologies and setting policies. . Primary tasks are to conduct reviews, as NCBI ORGANISMAL CLASSIFICATION NCBI organismal classification. An ontology representation of the NCBI organismal taxonomy. This ontology uses a mixed-case prefix. Identifiers and URIs should use "NCBITaxon". The NCBITaxon ontology is an automatic translation of the NCBI taxonomy database into obo/owl. The translation treats each taxon as an obo/owl class whose instances(for
OBO FOUNDRY MEMBERSHIP REQUIREMENTS AND TECHNICAL DETAILS Requirements for OBO Membership. A project should exist, with work started. We will not “pre-book” IDSPACEs and domains for potential future resources. A project must be doing original work within the biological ontology community. We will not provide an IDSPACE for a project that is issuing new identifier for existing ontologies. DOCUMENTED PLURALITY OF USERS (PRINCIPLE 9) Documented Plurality of Users (principle 9) Commitment To Collaboration (principle 10) Locus of Authority (principle 11) Naming Conventions (principle 12) Maintenance (principle 16) Responsiveness (principle 20) Ontologies. Ontology Table. ID Policy. HUMAN DEVELOPMENTAL ANATOMY, ABSTRACT OntoBee AberOWL OLS. A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20).EDITORIALWG
The OBO Foundry Editorial WG will: create guidelines for ontology review process (how we do reviews, operationally) create policies for ontology review criteria (what aspects of an ontology and which ontologies we should review) manage the ontology review process. Current activities are focused on creating guidelines for reviews. Toggle navigation The OBO FoundryToggle navigation
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OBO LIBRARY: FIND, USE, AND CONTRIBUTE TO COMMUNITY ONTOLOGIES The table below lists current OBO ontologies (in alphabetical order, but with the ontologies that have been manually reviewed by the OBO Foundry listed first, and obsolete ontologies listed last).Download table as:
bfo
Basic Formal Ontology The upper level ontology upon which OBO Foundry ontologies arebuilt. Detail
chebi
Chemical Entities of Biological Interest A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds. Detaildoid
Human Disease Ontology An ontology for describing the classification of human diseases organized by etiology. Detailgo
Gene Ontology
An ontology for describing the function of genes and gene productsDetail
obi
Ontology for Biomedical Investigations An integrated ontology for the description of life-science and clinical investigations Detailpato
Phenotype And Trait Ontology An ontology of phenotypic qualities (properties, attributes or characteristics) Detailpo
Plant Ontology
The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. Detailpr
PRotein Ontology (PRO) An ontological representation of protein-related entities Detailxao
Xenopus Anatomy Ontology XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis. Detailzfa
Zebrafish anatomy and development ontology A structured controlled vocabulary of the anatomy and development of the Zebrafish Detailaeo
Anatomical Entity Ontology AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology Detailagro
Agronomy Ontology
Ontology of agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments Detailamphx
The Amphioxus Development and Anatomy Ontology An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum). Detailapo
Ascomycete phenotype ontology A structured controlled vocabulary for the phenotypes of Ascomycete fungi Detailapollo_sv
Apollo Structured Vocabulary Defines terms and relations necessary for interoperation between epidemic models and public health application software that interface with these models Detailaro
Antibiotic Resistance Ontology Antibiotic resistance genes and mutations Detailbco
Biological Collections Ontology An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. Detailbspo
Biological Spatial Ontology An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces Detailbto
BRENDA tissue / enzyme source A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures. Detailcaro
Common Anatomy Reference Ontology An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species Detailcdao
Comparative Data Analysis Ontology a formalization of concepts and relations relevant to evolutionary comparative analysis Detailcheminf
Chemical Information Ontology Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them. Detailchiro
CHEBI Integrated Role Ontology CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes. Detailchmo
Chemical Methods Ontology CHMO, the chemical methods ontology, describes methods used toDetail
cido
Coronavirus Infectious Disease Ontology The Coronavirus Infectious Disease Ontology (CIDO) aims to ontologically represent and standardize various aspects of coronavirus infectious diseases, including their etiology, transmission, epidemiology, pathogenesis, diagnosis, prevention, and treatment.Detail
cl
Cell Ontology
The Cell Ontology is a structured controlled vocabulary for cell types in animals. Detailclao
Collembola Anatomy Ontology CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda). Detailclo
Cell Line Ontology
An ontology to standardize and integrate cell line information and to support computer-assisted reasoning. Detailclyh
Clytia hemisphaerica Development and Anatomy Ontology The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle. Detailcmo
Clinical measurement ontology Morphological and physiological measurement records generated from clinical and model organism research and health programs. Detailcob
Core Ontology for Biology and Biomedicine COB brings together key terms from a wide range of OBO projects to improve interoperability. Detailcro
Contributor Role Ontology A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability.Detail
cteno
Ctenophore Ontology
An anatomical and developmental ontology for ctenophores (CombJellies) Detail
cto
CTO: Core Ontology of Clinical Trials The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials. Detailcvdo
Cardiovascular Disease Ontology An ontology to describe entities related to cardiovasculardiseases Detail
ddanat
Dictyostelium discoideum anatomy A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum Detailddpheno
Dictyostelium discoideum phenotype ontology A structured controlled vocabulary of phenotypes of the slime-mould _Dictyostelium discoideum_. Detaildideo
Drug-drug Interaction and Drug-drug Interaction Evidence Ontology The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology Detaildpo
Drosophila Phenotype Ontology An ontology of commonly encountered and/or high level Drosophilaphenotypes. Detail
dron
The Drug Ontology
An ontology to support comparative effectiveness researchers studying claims data. Detailduo
Data Use Ontology
DUO is an ontology which represent data use conditions. Detailecao
The Echinoderm Anatomy and Development Ontology An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586). Detaileco
Evidence ontology
An ontology for experimental and other evidence statements. Detailecocore
An ontology of core ecological entities An ontology to provide core semantics for ecological entities.Detail
ecto
Environmental conditions, treatments and exposures ontology ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology). Detailemapa
Mouse Developmental Anatomy Ontology An ontology for mouse anatomy covering embryonic development and postnatal stages. Detailenvo
Environment Ontology Ontology of environmental features and habitats Detaileupath
VEuPathDB ontology
An ontology is developed to support Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB; https://veupathdb.org). Detailexo
Exposure ontology
Vocabularies for describing exposure data to inform understanding of environmental health. Detailfao
Fungal gross anatomy A structured controlled vocabulary for the anatomy of fungi.Detail
fbbi
Biological Imaging Methods Ontology A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. Detailfbbt
Drosophila gross anatomy An ontology representing the gross anatomy of Drosophila melanogaster. Detailfbcv
FlyBase Controlled Vocabulary A structured controlled vocabulary used for various aspects of annotation by FlyBase. Detailfbdv
Drosophila development A structured controlled vocabulary of the development of Drosophila melanogaster. Detailfideo
Food Interactions with Drugs Evidence Ontology Food-Drug interactions automatically extracted from scientificliterature Detail
flopo
Flora Phenotype Ontology Traits and phenotypes of flowering plants occurring in digitizedFloras Detail
fma
Foundational Model of Anatomy Ontology (subset) This is currently a slimmed down version of FMA Detailfoodon
FOODON
A broadly scoped ontology representing entities which bear a “food role”. It encompasses materials in natural ecosystems and food webs as well as human-centric categorization and handling offood. Detail
fovt
FuTRES Ontology of Vertebrate Traits FuTRES Ontology of Vertebrate Traits is an application ontology used to convert vertebrate trait data in spreadsheet to triples. FOVT leverages the BioCollections Ontology (BCO) to link observations of individual specimens to their trait values. Traits are defined in the Ontology of Biological Attributes (OBA). Detailfypo
Fission Yeast Phenotype Ontology FYPO is a formal ontology of phenotypes observed in fission yeast.Detail
gaz
Gazetteer
A gazetteer constructed on ontological principles Detailgecko
Genomics Cohorts Knowledge Ontology An ontology to represent genomics cohort attributes Detailgenepio
Genomic Epidemiology Ontology The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks. Detailgeno
Genotype Ontology
An integrated ontology for representing the genetic variations described in genotypes, and their causal relationships to phenotype and diseases. Detailgeo
Geographical Entity Ontology An ontology of geographical entities Detailgno
Glycan Naming and Subsumption Ontology (GNOme) GlyTouCan provides stable accessions for glycans described at varyious degrees of characterization, including compositions (no linkage) and topologies (no carbon bond positions or anomeric configurations). GNOme organizes these stable accessions for interative browsing, for text-based searching, and for automated reasoning with well-defined characterization levels. Detailhancestro
Human Ancestry Ontology The Human Ancestry Ontology (HANCESTRO) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies. Detailhao
Hymenoptera Anatomy Ontology A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants) Detailhom
Homology Ontology
This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology. Detailhsapdv
Human Developmental Stages Life cycle stages for Human Detailhtn
Hypertension Ontology An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines Detailiao
Information Artifact Ontology An ontology of information entities. Detailiceo
Integrative and Conjugative Element Ontology ICEO is an integrated biological ontology for the description of bacterial integrative and conjugative elements (ICEs). Detailico
Informed Consent Ontology An ontology of clinical informed consents Detailido
Infectious Disease Ontology A set of interoperable ontologies that will together provide coverage of the infectious disease domain. IDO core is the upper-level ontology that hosts terms of general relevance across the domain, while extension ontologies host terms to specific to a particular part of the domain. Detailino
Interaction Network Ontology An ontology of interactions and interaction networks Detaillabo
clinical LABoratory Ontology LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents. Detailma
Mouse adult gross anatomy A structured controlled vocabulary of the adult anatomy of themouse (Mus). Detail
maxo
Medical Action Ontology Medical Action Ontology is an ontology... Detailmco
Microbial Conditions Ontology Microbial Conditions Ontology is an ontology... Detailmf
Mental Functioning Ontology The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning. Detailmfmo
Mammalian Feeding Muscle Ontology The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors. Detailmfoem
Emotion Ontology
An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings. Detailmfomd
Mental Disease Ontology An ontology to describe and classify mental diseases such as schizophrenia, annotated with DSM-IV and ICD codes where applicableDetail
mi
Molecular Interactions Controlled Vocabulary A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. Detailmiapa
MIAPA Ontology
An application ontology to formalize annotation of phylogeneticdata. Detail
micro
Ontology of Prokaryotic Phenotypic and Metabolic Characters An ontology of prokaryotic phenotypic and metabolic charactersDetail
mmo
Measurement method ontology A representation of the variety of methods used to make clinical and phenotype measurements. Detailmmusdv
Mouse Developmental Stages Life cycle stages for Mus Musculus Detailmod
Protein modification PSI-MOD is an ontology consisting of terms that describe protein chemical modifications Detailmondo
Mondo Disease Ontology A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology. Detailmop
Molecular Process Ontology Processes at the molecular level Detailmp
Mammalian Phenotype Ontology Standard terms for annotating mammalian phenotypic data. Detailmpath
Mouse pathology ontology A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes Detailmpio
Minimum PDDI Information Ontology An ontology of minimum information regarding potential drug-drug interaction information. Detailmro
MHC Restriction Ontology An ontology for Major Histocompatibility Complex (MHC) restriction in experiments Detailnbo
Neuro Behavior Ontology An ontology of human and animal behaviours and behaviouralphenotypes Detail
ncbitaxon
NCBI organismal classification An ontology representation of the NCBI organismal taxonomy Detailncit
NCI Thesaurus OBO Edition NCI Thesaurus (NCIt)is a reference terminology that includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities. The NCIt OBO Edition aims to increase integration of the NCIt with OBO Library ontologies. NCIt OBO Edition releases should be considered experimental. Detailncro
Non-Coding RNA Ontology An ontology for non-coding RNA, both of biological origin, andengineered. Detail
nomen
NOMEN - A nomenclatural ontology for biological names NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature. Detailoae
Ontology of Adverse Events A biomedical ontology in the domain of adverse events Detailoarcs
Ontology of Arthropod Circulatory Systems OArCS is an ontology describing the Arthropod ciruclatory system.Detail
oba
Ontology of Biological Attributes A collection of biological attributes (traits) covering all kingdoms of life. Detailobcs
Ontology of Biological and Clinical Statistics A biomedical ontology in the domain of biological and clinicalstatistics. Detail
obib
Ontology for Biobanking An ontology built for annotation and modeling of biobank repository and biobanking administration Detailogg
The Ontology of Genes and Genomes A formal ontology of genes and genomes of biological organisms.Detail
ogms
Ontology for General Medical Science An ontology for representing treatment of disease and diagnosis and on carcinomas and other pathological entities Detailogsf
Ontology of Genetic Susceptibility Factor An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process. Detailohd
The Oral Health and Disease Ontology The Oral Health and Disease Ontology was created, initially, to represent the content of dental practice health records. Detailohmi
Ontology of Host-Microbiome Interactions The Ontology of Host-Microbiome Interactions aims to ontologically represent and standardize various entities and relations related to microbiomes, microbiome host organisms (e.g., human and mouse), and the interactions between the hosts and microbiomes at differentconditions. Detail
ohpi
Ontology of Host Pathogen Interactions OHPI is a community-driven ontology of host-pathogen interactions (OHPI) and represents the virulence factors (VFs) and how the mutants of VFs in the Victors database become less virulence inside a host organism or host cells. It is developed to represent manually curated HPI knowledge available in the PHIDIAS resource. Detailolatdv
Medaka Developmental Stages Life cycle stages for Medaka Detailomiabis
Ontologized MIABIS
An ontological version of MIABIS (Minimum Information About BIobank data Sharing) Detailomit
Ontology for MIRNA Target Ontology to establish data exchange standards and common data elements in the microRNA (miR) domain Detailomo
OBO Metadata Ontology An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO). Detailomp
Ontology of Microbial Phenotypes An ontology of phenotypes covering microbes Detailomrse
Ontology of Medically Related Social Entities This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations. Detailone
Ontology for Nutritional Epidemiology An ontology to standardize research output of nutritional epidemiologic studies. Detailons
ONS
An ontology for description of concepts in the nutritional studiesdomain. Detail
ontoneo
Obstetric and Neonatal Ontology The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, andof her baby. Detail
oostt
Ontology of Organizational Structures of Trauma centers and Traumasystems
An ontology built for representating the organizational components of trauma centers and trauma systems. Detailopl
Ontology for Parasite LifeCycle A reference ontology for parasite life cycle stages. Detailopmi
Ontology of Precision Medicine and Investigation The Ontology of Precision Medicine and Investigation (OPMI) aims to ontologically represent and standardize various entities and relations associated with precision medicine and related investigations at different conditions. Detailornaseq
Ontology of RNA Sequencing An application ontology designed to annotate next-generation sequencing experiments performed on RNA. Detailovae
Ontology of Vaccine Adverse Events A biomedical ontology in the domain of vaccine adverse events.Detail
pco
Population and Community Ontology An ontology about groups of interacting organisms such as populations and communities Detailpdro
The Prescription of Drugs Ontology An ontology to describe entities related to prescription of drugsDetail
pdumdv
Platynereis Developmental Stages Life cycle stages for Platynereis dumerilii Detailpeco
Plant Experimental Conditions Ontology A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments. Detailphipo
Pathogen Host Interaction Phenotype Ontology PHIPO is a formal ontology of species-neutral phenotypes observed in pathogen-host interactions. Detailplana
planaria-ontology
PLANA, the planarian anatomy ontology, encompasses the anatomy and life cycle stages for both __Schmidtea mediterranea__ biotypes. Detailplanp
Planarian Phenotype Ontology Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea. Detailporo
Porifera Ontology
An ontology covering the anatomy of the taxon Porifera (sponges)Detail
ppo
Plant Phenology Ontology An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales. Detailpsdo
Performance Summary Display Ontology Ontology to reproducibly study visualizations of clinicalperformance Detail
pso
Plant Stress Ontology The Plant Stress Ontology describes... Detailpw
Pathway ontology
A controlled vocabulary for annotating gene products to pathways.Detail
ro
Relation Ontology
Relationship types shared across multiple ontologies Detailrs
Rat Strain Ontology
Ontology of rat strains Detailrxno
Name Reaction Ontology Connects organic name reactions to their roles in an organic synthesis and to processes in MOP Detailsepio
Scientific Evidence and Provenance Information Ontology An ontology for representing the provenance of scientific claims and the evidence that supports them. Detailso
Sequence types and features ontology A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases. Detailspd
Spider Ontology
An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow). Detailstato
The Statistical Methods Ontology STATO is a general-purpose STATistics Ontology. Its aim is to provide coverage for processes such as statistical tests, their conditions of application, and information needed or resulting from statistical methods, such as probability distributions, variables, spread and variation metrics. STATO also covers aspects of experimental design and description of plots and graphical representations commonly used to provide visual cues of data distribution or layout and to assist review of the results. Detailsymp
Symptom Ontology
An ontology of disease symptoms, with symptoms encompasing perceived changes in function, sensations or appearance reported by a patient indicative of a disease. Detailtaxrank
Taxonomic rank vocabulary A vocabulary of taxonomic ranks (species, family, phylum, etc)Detail
to
Plant Trait Ontology A controlled vocabulary of describe phenotypic traits in plants.Detail
trans
Pathogen Transmission Ontology An ontology representing the disease transmission process during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host. Detailtto
Teleost taxonomy ontology An ontology covering the taxonomy of teleosts (bony fish) Detailuberon
Uberon multi-species anatomy ontology An integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies Detailuo
Units of measurement ontology Metrical units for use in conjunction with PATO Detailupheno
Unified phenotype ontology (uPheno) The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology. Detailvo
Vaccine Ontology
VO is a biomedical ontology in the domain of vaccine andvaccination. Detail
vto
Vertebrate Taxonomy Ontology Comprehensive hierarchy of extinct and extant vertebrate taxa.Detail
wbbt
C. elegans Gross Anatomy Ontology A structured controlled vocabulary of the anatomy of _Caenorhabditis elegans_. Detailwbls
C. elegans development ontology A structured controlled vocabulary of the development of _Caenorhabditis elegans_. Detailwbphenotype
C. elegans phenotype A structured controlled vocabulary of _Caenorhabditis elegans_phenotypes Detail
xco
Experimental condition ontology Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms. Detailxpo
Xenopus Phenotype Ontology XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis. Detailzeco
Zebrafish Experimental Conditions Ontology Experimental conditions applied to zebrafish, developed to facilitate experiment condition annotation at ZFIN Detailzp
Zebrafish Phenotype Ontology The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism. Detailcio
Confidence Information Ontology An ontology to capture confidence information about annotations.Detail
ero
eagle-i resource ontology An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens. Detailfobi
FOBI
FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data Detailgsso
Gender, Sex, and Sexual Orientation (GSSO) ontology The Gender, Sex, and Sexual Orientation (GSSO) ontology has terms for annotating interdisciplinary information concerning gender, sex, and sexual orientation for primary usage in the biomedical and adjacent sciences. Detailhp
Human Phenotype Ontology A structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease. Detailkisao
Kinetic Simulation Algorithm Ontology A classification of algorithms available for the simulation of models in biology. Detailmamo
Mathematical modeling ontology The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. Detailms
Mass spectrometry ontology A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry. Detailsbo
Systems Biology Ontology Terms commonly used in Systems Biology, and in particular in computational modeling. Detailswo
Software ontology
The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community. Detailtxpo
Toxic Process Ontology TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity. Detailvt
Vertebrate trait ontology An ontology of traits covering vertebrates Detailxlmod
HUPO-PSI cross-linking and derivatization reagents controlledvocabulary
A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry. Detailzfs
Zebrafish developmental stages ontology Developmental stages of the Zebrafish Detailsibo
Social Insect Behavior Ontology Social Behavior in insects Detailfix
Physico-chemical methods and properties An ontology of physico-chemical methods and properties. Detailogi
Ontology for genetic interval An ontology that formalizes the genomic element by defining an upper class genetic interval Detailrex
Physico-chemical process An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. Detailvario
Variation Ontology
Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms ofvariations. Detail
ceph
Cephalopod Ontology
An anatomical and developmental ontology for cephalopods inactiveDetail
ehdaa2
Human developmental anatomy, abstract A structured controlled vocabulary of stage-specific anatomical structures of the developing human. inactive Detailrnao
RNA ontology
Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures. inactive Detailupa
Unipathway
A manually curated resource for the representation and annotation of metabolic pathways inactive Detailcmf
CranioMaxilloFacial ontologyinactive Detail
idomal
Malaria Ontology
An application ontology to cover all aspects of malaria as well as the intervention attempts to control it. inactive Detailmiro
Mosquito insecticide resistance Application ontology for entities related to insecticide resistance in mosquitos inactive Detailtads
Tick Anatomy Ontology The anatomy of the Tick, _Families: Ixodidae, Argassidae_ inactiveDetail
tgma
Mosquito gross anatomy ontology A structured controlled vocabulary of the anatomy of mosquitoes.inactive Detail
bcgo
Beta Cell Genomics Ontology An application ontology built for beta cell genomics studies.obsolete Detail
dinto
The Drug-Drug Interactions Ontology A formal represention for drug-drug interactions knowledge.obsolete Detail
eo
Plant Environment Ontology A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments. obsolete Detailtao
Teleost Anatomy Ontology Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa obsolete Detailaao
Amphibian gross anatomyobsolete Detail
adw
Animal natural history and life historyobsolete Detail
aero
Adverse Event Reporting Ontology The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events obsolete Detailato
Amphibian taxonomy
obsolete Detail
bila
Bilateria anatomy
obsolete Detail
bootstrep
Gene Regulation Ontologyobsolete Detail
dc_cl
Dendritic cell
obsolete Detail
ehda
Human developmental anatomy, timed versionobsolete Detail
ehdaa
Human developmental anatomy, abstract versionobsolete Detail
emap
Mouse gross anatomy and development, timed A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus). obsolete Detailev
eVOC (Expressed Sequence Annotation for Humans)obsolete Detail
fbsp
Fly taxonomy
The taxonomy of the family _Drosophilidae_ (largely after Baechli) and of other taxa referred to in FlyBase. obsolete Detailflu
Influenza Ontology
obsolete Detail
gro
Cereal Plant Gross Anatomyobsolete Detail
habronattus
Habronattus courtshipobsolete Detail
imr
Molecule role (INOH Protein name/family name ontology)obsolete Detail
ipr
Protein Domains
obsolete Detail
lipro
Lipid Ontology
An ontology representation of the LIPIDMAPS nomenclature classification. obsolete Detailloggerhead
Loggerhead nesting
obsolete Detail
mao
Multiple alignment
obsolete Detail
mat
Minimal anatomical terminologyobsolete Detail
mfo
Medaka fish anatomy and development A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, _Oryzias latipes_. obsolete Detailmirnao
microRNA Ontology
An application ontology for use with miRNA databases. obsoleteDetail
mo
Microarray experimental conditions A standardized description of a microarray experiment in support of MAGE v.1. obsolete Detailnif_cell
NIF Cell
Neuronal cell types obsolete Detailnif_dysfunction
NIF Dysfunction
obsolete Detail
nif_grossanatomy
NIF Gross Anatomy
obsolete Detail
nmr
NMR-instrument specific component of metabolomics investigations Descriptors relevant to the experimental conditions of the Nuclear Magnetic Resonance (NMR) component in a metabolomics investigation.obsolete Detail
obo_rel
OBO relationship types (legacy)obsolete Detail
pao
Plant Anatomy Ontologyobsolete Detail
pd_st
Platynereis stage ontologyobsolete Detail
pgdso
Plant Growth and Development Stageobsolete Detail
plo
Plasmodium life cycleobsolete Detail
propreo
Proteomics data and process provenanceobsolete Detail
resid
Protein covalent bond For the description of covalent bonds in proteins. obsolete Detailsao
Subcellular anatomy ontologyobsolete Detail
sep
Sample processing and separation techniques A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments.obsolete Detail
sopharm
Suggested Ontology for Pharmacogenomicsobsolete Detail
tahe
Terminology of Anatomy of Human Embryologyobsolete Detail
tahh
Terminology of Anatomy of Human Histologyobsolete Detail
vsao
Vertebrate Skeletal Anatomy Ontology- Vertebrate skeletal anatomy ontology. obsolete Detailypo
Yeast phenotypes
obsolete Detail
zea
Maize gross anatomy
obsolete Detail
epo
Epidemiology Ontology An ontology designed to support the semantic annotation of epidemiology resources obsolete Detailiev
Event (INOH pathway ontology)obsolete Detail
vhog
Vertebrate Homologous Ontology Group Ontologyobsolete Detail
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