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http://purl.bioontology.org/ontology/MEO

Ontology for organismal habitats (especially focused on microbes)

Proper citation: Metagenome and Microbes Environmental Ontology (RRID:SCR_010359) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/MIXSCV

Controlled vocabularies for the MIxS (Minimal Information about any Sequence) family of metadata checklists. See http://gensc.org/gc_wiki/index.php/MIxS for details on the MIxS checklists.

Proper citation: Minimal Information about any Sequence Controlled Vocabularies (RRID:SCR_010363) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/PMR

Ontology for knowledge representation related to computer-based decision support in rehabilitation; concepts and relationships in the rehabilitation domain, integrating clinical practice, the ICD (specifically its 11th revision), the clinical investigator record ontology, the ICF and SNOMED CT.

Proper citation: Physical Medicine and Rehabilitation (RRID:SCR_005948) Copy   

•   Source: SciCrunch Registry

http://www.human-phenotype-ontology.org/

Provides standardized vocabulary of phenotypic abnormalities encountered in human disease. Structured and controlled vocabulary for phenotypic features encountered in human hereditary and other disease. HPO is being developed in collaboration with members of OBO Foundry (Open Biological and Biomedical Ontologies), and logical definitions for HPO terms are being developed using PATO and a number of other ontologies including FMA, GO, ChEBI, and MPATH.

Proper citation: Human Phenotype Ontology (RRID:SCR_006016) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/RSA

An ontology for sequence annotations and how to preserve them with reference sequences.

Proper citation: Reference Sequence Annotation (RRID:SCR_006095) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/VO

A biomedical ontology in the vaccine domain

Proper citation: Vaccine Ontology (RRID:SCR_006271) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/DERMO

Ontology of human dermatologic disease

Proper citation: Human Dermatological Disease Ontology (RRID:SCR_007648) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/HPIO

Ontology for host pathogen interactions in farmed animals

Proper citation: Host Pathogen Interactions Ontology (RRID:SCR_007647) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/BSPO

A small ontology for anatomical spatial references, such as dorsal, ventral, axis, and so forth.

Proper citation: Spatial Ontology (RRID:SCR_007860) Copy   

•   Source: SciCrunch Registry

http://mged.sourceforge.net/ontologies/MGEDontology.php

An ontology including concepts, definitions, terms, and resources for a standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1. These terms will enable structure queries of elements of the experiments. Furthermore, the terms will also enable unambiguous descriptions of how the experiment was performed.

Proper citation: MGED Ontology (RRID:SCR_004484) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/PHENX

Ontology for standard measures related to complex diseases, phenotypic traits and environmental exposures

Proper citation: PhenX Phenotypic Terms (RRID:SCR_004518) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/ONTOPNEUMO

Ontology of pneumology (french version) developped by Audrey Baneyx, under the direction of Jean Charlet about knowledge engineering expertise and by Francois-Xavier Blanc in collaboration with Bruno Housset about medical expertise.

Proper citation: Ontology of Pneumology (RRID:SCR_004378) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/PVONTO

A pharmacovigilance ontology to connect known facts on drugs, disease, ADEs, and their molecular mechanisms.

Proper citation: Pharmacovigilance Ontology (RRID:SCR_004499) Copy   

•   Source: SciCrunch Registry

http://sequenceontology.org/

A collaborative ontology for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. The OBO revision is available here: http://sourceforge.net/p/song/svn/HEAD/tree/ SO includes different kinds of features which can be located on the sequence. Biological features are those which are defined by their disposition to be involved in a biological process. Biomaterial features are those which are intended for use in an experiment such as aptamer and PCR_product. There are also experimental features which are the result of an experiment. SO also provides a rich set of attributes to describe these features such as polycistronic and maternally imprinted. The Sequence Ontologies use the OBO flat file format specification version 1.2, developed by the Gene Ontology Consortium. The ontology is also available in OWL from Open Biomedical Ontologies. This is updated nightly and may be slightly out of sync with the current obo file. An OWL version of the ontology is also available. The resolvable URI for the current version of SO is http://purl.obolibrary.org/obo/so.owl.

Proper citation: SO (RRID:SCR_004374) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/OBOREL

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Ontology that defines core relations used in all OBO ontologies. Obsolete. Replaced with RO.

Proper citation: Open Biological and Biomedical Ontologies Relationship Types (RRID:SCR_004409) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/searches/MP_form.shtml

Community ontology to provide standard terms for annotating mammalian phenotypic data. It has a hierarchical structure that permits a range of detail from high-level, broadly descriptive terms to very low-level, highly specific terms. This range is useful for annotating phenotypic data to the level of detail known and for searching for this information using either broad or specific terms as search criteria. Your input is welcome.

Proper citation: MPO (RRID:SCR_004855) Copy   

•   Source: SciCrunch Registry

http://www.nlm.nih.gov/mesh

A controlled vocabulary thesaurus that consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. MeSH, in machine-readable form, is provided at no charge via electronic means. MeSH descriptors are arranged in both an alphabetic and a hierarchical structure. At the most general level of the hierarchical structure are very broad headings such as Anatomy or Mental Disorders. More specific headings are found at more narrow levels of the twelve-level hierarchy, such as Ankle and Conduct Disorder. There are 27,149 descriptors in 2014 MeSH. There are also over 218,000 entry terms that assist in finding the most appropriate MeSH Heading, for example, Vitamin C is an entry term to Ascorbic Acid. In addition to these headings, there are more than 219,000 headings called Supplementary Concept Records (formerly Supplementary Chemical Records) within a separate thesaurus. The MeSH thesaurus is used by NLM for indexing articles from 5,400 of the world''''s leading biomedical journals for the MEDLINE/PubMED database. It is also used for the NLM-produced database that includes cataloging of books, documents, and audiovisuals acquired by the Library. Each bibliographic reference is associated with a set of MeSH terms that describe the content of the item. Similarly, search queries use MeSH vocabulary to find items on a desired topic.

Proper citation: MeSH (RRID:SCR_004750) Copy   

•   Source: SciCrunch Registry

http://www.obofoundry.org/ontology/pato.html

Ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation. The new PATO differs from the old in that the system of attributes and values has been abandoned in favor of a single hierarchy of qualities. PATO is designed to be used in conjunction with ontologies of quality-bearing entities. An example of such an entity is an insect eye (taken from the fly_anatomy ontology), which could be the bearer of the quality ''red'' (PATO:0000322). This combination is the red eye phenotype. We say that the phenotype term is ''post-coordinated'', as it is formed by coordinating two terms together. This is in contrast to ontologies of pre-coordinated phenotypes, such as the Mammalian Phenotype (MP) ontology. PATO is independent of any exchange format or database schema. One way of expressing phenotype annotation using PATO is pheno-syntax, or pheno-xml. They will also post recommendations for representing phenotypes using OWL. All representations share the same basic formal underpinnings, a combination of quality-bearing entity and a quality (the EQ model).

Proper citation: PATO (RRID:SCR_004782) Copy   

•   Source: SciCrunch Registry

http://www.ifomis.org/bfo

A small, upper level ontology that is designed for use in supporting information retrieval, analysis and integration in scientific and other domains. BFO is a genuine upper integration in scientific and other domains. Thus it does not contain physical, chemical, biological or other terms which would properly fall within the coverage domains of the special sciences.

Proper citation: BFO (RRID:SCR_004818) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/OBIWS

Ontology that extends the Ontology for Biomedical Investigations (OBI) to support consistent annotation of Bioinformatics Web services.

Proper citation: Bioinformatics Web Service Ontology (RRID:SCR_004529) Copy   

•   Source: SciCrunch Registry