format-version: 1.2
date: 30:07:2008 15:14
saved-by: wablo
auto-generated-by: OBO-Edit 1.002
remark: Metaonto is a meta-ontology that has OBO ontologies as it's terms.

[Term]
id: METAONTO:0000001
name: OBO ontology
def: "An OBO ontology is a science-based ontology that was established following a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain." [http://www.obofoundry.org/]

[Term]
id: METAONTO:0010001
name: Amphibian gross anatomy
def: "A structured controlled vocabulary of the anatomy of Amphibians." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=amphibian_anatomy]
synonym: "AAO" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010002
name: Spatial Ontology
def: "A small ontology for anatomical spatiol references, such as dorsal, ventral, axis, and so forth." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=spatial]
synonym: "BSPO" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010003
name: Common Anatomy Reference Ontology
def: "The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO will be described in Anatomy Ontologies for Bioinformatics: Principles and Practice Albert Burger, Duncan Davidson and Richard Baldock (Editors)" [http://www.obofoundry.org/cgi-bin/detail.cgi?id=caro]
synonym: "CARO" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010004
name: Chemical entities of biological interest
def: "A structured classification of chemical compounds of biological relevance." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=chebi]
synonym: "CHEBI" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010005
name: Cell type
def: "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. This ontology is not organism specific; indeed it includes cell types from prokaryotes to mammals, including plants and fungi. A full description of the Cell Ontology can be found in Bard, Rhee and Ashburner. 2005. An Ontology for Cell Types." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell]
synonym: "CL" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010006
name: Dictyostelium discoideum anatomy
def: "A structured controlled vocabulary of the anatomy of the slime-mould Dictyostelium discoideum." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=dictyostelium_discoideum_anatomy]
synonym: "DDANAT" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010007
name: Human disease
def: "Creating a comprehensive hierarchical controlled vocabulary for human disease representation." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=disease_ontology]
synonym: "DOID" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010008
name: Evidence codes
def: "A rich ontology for experimental and other evidence statements." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=evidence_code]
synonym: "ECO" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010009
name: Human developmental anatomy, timed version
def: "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). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=human-dev-anat-staged]
synonym: "EHDA" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010010
name: Human developmental anatomy, abstract version
def: "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). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=human-dev-anat-abstract]
synonym: "EHDAA" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010011
name: Mouse gross anatomy and development
def: "A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus)." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=emap]
synonym: "EMAP" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010012
name: Environment Ontology
def: "Ontology of environmental features and habitats" [http://www.obofoundry.org/cgi-bin/detail.cgi?id=envo]
synonym: "ENVO" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010013
name: Fungal gross anatomy
def: "A structured controlled vocabulary for the anatomy of fungi." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fungal_anatomy]
synonym: "FAO" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010014
name: Drosophila gross anatomy
def: "A structured controlled vocabulary of the anatomy of Drosophila melanogaster." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fly_anatomy]
synonym: "FBbt" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010015
name: Drosophila development
def: "A structured controlled vocabulary of the development of Drosophila melanogaster." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fly_development]
synonym: "FBdv" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010016
name: Fly taxonomy
def: "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fly_taxonomy]
synonym: "FBsp" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010017
name: Foundational Model of Anatomy (subset)
def: "Obo format translation of the FMA, omitting all relationships other than is_a, part_of and has_part. Future versions of fma_obo will include more relationships" [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fma_lite]
synonym: "FMA" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010018
name: Gene ontology
def: "Provides structured controlled vocabularies for the annotation of gene products with respect to their biological role, molecular function and cellular location." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=biological_process]
synonym: "GO" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010019
name: Infectious disease
def: "A structured controlled vocabulary for infectuous diseases." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=infectious_disease_ontology]
synonym: "IDO" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010020
name: Mouse adult gross anatomy
def: "A structured controlled vocabulary of the adult anatomy of the mouse (Mus)." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=adult_mouse_anatomy]
synonym: "MA" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010021
name: Medaka fish anatomy and development
def: "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=medaka_anatomy_development]
synonym: "MFO" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010022
name: Protein-protein interaction
def: "A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. Developed by the HUPO Proteomics Standards Initiative." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=psi-mi]
synonym: "MI" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010023
name: Mosquito insecticide resistance
def: "Application ontology for entities related to insecticide resistance in mosquitos" [http://www.obofoundry.org/cgi-bin/detail.cgi?id=mosquito_insecticide_resistance]
synonym: "MIRO" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010024
name: Protein modification
def: "PSI-MOD is an ontology consisting of terms that describe protein chemical modifications, logically linked by an is_a relationship in such a way as to form a direct acyclic graph (DAG). The PSI-MOD ontology has more than 45 top-level nodes, and provides alternative hierarchical paths for classifying protein modifications either by the molecular structure of the modification, or by the amino acid residue that is modified." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=psi-mod]
synonym: "MOD" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010025
name: Mammalian phenotype
def: "The Mammalian Phenotype Ontology is under development as a community effort to provide standard terms for annotating mammalian phenotypic data." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=mammalian_phenotype]
synonym: "MP" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010026
name: Mouse pathology
def: "A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes" [http://www.obofoundry.org/cgi-bin/detail.cgi?id=mouse_pathology]
synonym: "MPATH" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010027
name: Ontology for biomedical investigations
def: "OBI models the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. This project was formerly titled the Functional Genomics Investigation Ontology (FuGO) project." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=obi]
synonym: "OBI" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010028
name: OBO relationship types
def: "Defines core relations used in all OBO ontologies." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=relationship]
synonym: "OBO_REL" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010029
name: Phenotypic quality
def: "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, edematous and arrested." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=quality]
synonym: "PATO" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010030
name: Plant ontology
def: "A controlled vocabulary of growth and developmental stages in various plants and of plant morphological and anatomical structures representing organs, tissues, cell types, and their biological relationships based on spatial and developmental organization. The plant ontologies, which includes both the plant structure and growth and development stages can be downloaded as a single file in OBO format." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=po_temporal]
synonym: "PO" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010031
name: Protein ontology
def: "Protein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes (ontology for ProEvo), to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies" [http://www.obofoundry.org/cgi-bin/detail.cgi?id=protein]
synonym: "PRO" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010032
name: Subcellular anatomy ontology
def: "We have developed the Subcellular Anatomy Ontology for the Nervous System (SAO) to provide a formal ontology to describe structures from the dimensional range known as the oemesoscale, encompassing cellular and subcellular structure, supracellular domains, and macromolecules. The SAO describes the parts of neurons and glia and how these parts come together to define supracellular structures such as synapses and neuropil (Fong et al., submitted). Molecular specializations of each compartment and cell type are identified. The SAO was designed with the goal of providing a means to annotate cellular and subcellular data obtained from light and electron microscopy, including assigning macromolecules to their approporiate subcellular domains. The SAO thus provides a bridge between ontologies that describe molecular species and those concerned with more gross anatomical scales. Because it is intended to integrate into ontological efforts at these other scales, particular care was taken to construct the ontology in a way that supports such integration." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=sao]
synonym: "SAO" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010033
name: Systems Biology
def: "The Systems Biology Ontology aims to strictly index and define terms used in quantitative biochemistry. The ontology is made up of four orthogonal vocabularies. A controlled vocabulary defines the roles of reaction participants, such as 'substrate', 'catalyst', etc. A taxonomy orders the quantitative parameters used in biochemistry such as 'Michaelis constant', but also 'first-order forward rate constant'. A precise classification of rate laws defines them, such as 'first-order reversible mass action kinetics'. Each term contains a precise mathematical expression stored as a MathML lambda function. Finally, a list of simulation frameworks, such as 'discrete' or 'continuous' precises the validity of a rate-law. The Systems Biology Ontology can be used to increase the semantic content of quantitative models. SBO vocabularies can also be used to annotate results of biochemical experiments in order to facilitate their efficient reuse." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=systems_biology]
synonym: "SBO" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010034
name: Sequence types and features
def: "The Sequence Ontology provides a structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases. SOFA is a minimal version of SO for use in data exchange." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=sequence]
synonym: "SO" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010035
name: Suggested Ontology for Pharmacogenomics
def: "SO-Pharm is a formal ontology that represent domain knowledge in pharmacogenomics. To achieve this goal SO-Pharm articulates ontologies from sub domains of phamacogenomics (i.e. genotype, phenotype, drug, trial representations). SO-Pharm enables to support knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=pharmacogenomics]
synonym: "SOPHARM" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010036
name: Spider Ontology
def: "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)." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=spider_anatomy]
synonym: "SPD" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010037
name: Tick gross anatomy
def: "The anatomy of the Tick, Families: Ixodidae, Argassidae" [http://www.obofoundry.org/cgi-bin/detail.cgi?id=tick_anatomy]
synonym: "TADS" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010038
name: Teleost anatomy and development
def: "Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa" [http://www.obofoundry.org/cgi-bin/detail.cgi?id=teleost_anatomy]
synonym: "TAO" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010039
name: Mosquito gross anatomy
def: "A structured controlled vocabulary of the anatomy of mosquitoes." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=mosquito_anatomy]
synonym: "TGMA" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010040
name: Cereal plant trait
def: "A controlled vocabulary of describe phenotypic traits in cereal plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature cereal plant." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=plant_trait]
synonym: "TO" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010041
name: Pathogen transmission
def: "This vocabulary describes a process that is the means of how a pathogen is transmitted from one host, reservoir, or source to another host. This transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles. " [http://www.obofoundry.org/cgi-bin/detail.cgi?id=transmission]
synonym: "TRANS" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010042
name: Teleost taxonomy
def: "The Teleost taxonomy ontology is being used to facilitate annotation of phenotypes, particularly for taxa that are not covered by NCBI because no submissions of molecular data have been made. Taxonomy ontologies can also be valuable in annotating legacy data, where authors make phenotype or ecological assertions (e.g., host-parasite associations) that refer to groups that are reorganized or no longer recognized. The taxonomy ontology serves as the source of taxa for our project's use for identifying evolutionary changes that match the phenotype of a zebrafish mutant." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=teleost_taxonomy]
synonym: "TTO" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010043
name: Units of measurement
def: "Metrical units for use in conjunction with PATO" [http://www.obofoundry.org/cgi-bin/detail.cgi?id=unit]
synonym: "UO" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010044
name: C. elegans gross anatomy
def: "A structured controlled vocabulary of the anatomy of Caenorhabditis elegans." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=worm_anatomy]
synonym: "WBbt" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010045
name: C. elegans development
def: "A structured controlled vocabulary of the development of Caenorhabditis elegans." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=worm_development]
synonym: "WBls" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010046
name: C. elegans phenotype
def: "A structured controlled vocabulary of Caenorhabditis elegans phenotypes" [http://www.obofoundry.org/cgi-bin/detail.cgi?id=worm_phenotype]
synonym: "WBPhenotype" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010047
name: Xenopus anatomy and development
def: "A structured controlled vocabulary of the anatomy and development of the African clawed frog (Xenopus laevis)." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=xenopus_anatomy]
synonym: "XAO" EXACT []
is_a: METAONTO:0000001 ! OBO ontology

[Term]
id: METAONTO:0010048
name: Zebrafish anatomy and development
def: "A structured controlled vocabulary of the anatomy and development of the Zebrafish (Danio rerio)." [http://www.obofoundry.org/cgi-bin/detail.cgi?id=zebrafish_anatomy]
synonym: "ZFA" EXACT []
is_a: METAONTO:0000001 ! OBO ontology