MGED Ontology Resources

• Ontology resources for different species
  
• Resources for ontology concepts
  
• Ontology resources for array design
  
• A brief review of clinical vocabularies listed here. Courtesy Michael Krauthammer, Columbia U.
  
• Sample description using the concepts and sources listed below (courtesy of M. Hofmann and S. Schmidtke, LION bioscience AG).
• Microarray descriptions (besides sample or biomaterial) from MAGE requiring inclusion into the MGED ontology. Courtesy Jason Stewart, OpenInformatics

• Arabidopsis thaliana:
  ABRC: Arabidopsis Biological Resource Center.

  AFGC: The Arabidopsis Functional Genomics Consortium has sample forms for Experiment Information and RNA Classification. Sample descriptions are included in RNA Classification.

  TAIR: The Arabidopsis Information Resource. Ontologies and controlled vocabularies for gene annotation.

• Bacteria and archea:
  CABRI: Common Access to Biological Resources and Information. Data input & authentication for bacteria and archea.

• Caenorhabditis elegans:
  C elegans Parts Index: List of all cells.

  Cytomer: A database on gene expression sources.

  Lifestage system - GOBO version.

  WormBase Pedigree Browser: Cell groups and lineage.

• Chicken (taxon-Gallus gallus):
  UNSW Embryology Chicken Development The University of New South Wales Embryology Resource developed for Revision of concepts in embryological development.

• Drosophila:
  FlyBase: A Database of the Drosophila Genome. Controlled vocabularies.

  FlyBase anatomy and ontogeny - GOBO version.

• Filamentous fungi and yeasts:
  CABRI: Common Access to Biological Resources and Information. Data input & authentication for filamentous fungi and yeasts.

• Homo sapiens:
  CBIL's Controlled Vocabularies: The controlled vocabulary is based on a table of anatomy terms taken from the Mouse Gene Expression Database at the Jackson Laboratory (specifically GXD mouse stage 28 - adult.) However, it has been extended to incorporate human anatomy and also revised in a number of areas, particularly the haematolymphoid system, based on the 37th edition of Gray's Anatomy.

  Cytomer: A database on gene expression sources.

  GALEN: GALEN is a radical new technology for medical coding and terminology.

  Histobank: The interactive histology atlas.

  Human Developmental Anatomy: This Human Atlas has been designed to identify those tissues present in human embryos during the first 50 or so days of development (Carnegie Stages 1-20). The Atlas can be viewed in two formats. First, the basic anatomical data designed to provide standards for analysing normal and congenitally abnormal human embryos (this page). Secondly a more detailed format (it includes additional sub-tissue regions) which is designed to be used as the terminology for gene-expression database(s). This second format is intended to be compatible with the anatomical terminology and organisation used for storing gene-expression data in the Mouse Atlas Project. (There is also a comparison chart which links mouse and human developmental stages.)

  International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM): The International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) is based on the World Health Organization's Ninth Revision, International Classification of Diseases (ICD-9). ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States. The ICD-9 is used to code and classify mortality data from death certificates.
  [Note: see also the ICD-9 classification in KEGG that is supplemented with disease genes.

  The IUPS Physiome Project: Publications, data, models, images and movies can be accessed from here via several alternative ontological trees.

  Systematized Nomenclature of Medicine (SNOMED): SNOMED International, a division of the College of American Pathologists (CAP), oversees the strategic direction and scientific maintenance of the Systematized Nomenclature of Medicine, better known as SNOMED®. Over the last 35 years SNOMED works have become recognized globally as a comprehensive, multiaxial, controlled terminology created for the indexing of the entire medical record.

  NTP Code Tables: Standard nomenclature for National Toxicology Program clinical observations and gross and micropathology. TDMS Database Pathology Code Table - Microscopic Terms

  National Toxicology Program. Clinical measurements.

• Maize:
  MaizeDB:Whole Plant, Phenotype, Trait Variance. This page enables you to review the current list of very diverse traits and their phenotypes currently in the Maize database (MaizeDB).

• Mouse:
  CBIL's Controlled Vocabularies: The controlled vocabulary is based on a table of anatomy terms taken from the Mouse Gene Expression Database at the Jackson Laboratory (specifically GXD mouse stage 28 - adult.) However, it has been extended to incorporate human anatomy and also revised in a number of areas, particularly the haematolymphoid system, based on the 37th edition of Gray's Anatomy.

  Edinburgh Mouse Atlas: Theiler Stage Selection.

  EMAP - GOBO version: The Anatomical Dictionary for Mouse Development has been developed at the Department of Anatomy, University of Edinburgh, Scotland and the MRC Human Genetics Unit, Edinburgh as part of the Edinburgh Mouse Atlas project (EMAP), in collaboration with the Gene Expression (GXD) project at MGI, The Jackson Laboratory, Bar Harbor, ME.

  Histobank: The interactive histology atlas.

  International Committe on Standard Genetic Nomenclature for Mice Rules for nomenclature of inbred strains.

  The Mouse Anatomical Dictionary: Stages 1 through 26 (embryonic development) of the Standard Anatomical Nomenclature Database are being developed at the Department of Anatomy, University of Edinburgh, Scotland and the MRC Human Genetics Unit, Edinburgh, as part of the The Mouse Atlas and 3D Graphical Gene Expression Database Project. Copyright 1998 University of Edinburgh (UK) and MRC (UK). Questions and comments should be sent to Jonathan Bard. Supported by the MRC, the BBSRC, and by the European Science Foundation. Stages 27 and 28 (newborn and postnatal mouse) are being developed by the Gene Expression Database Project at The Jackson Laboratory.

  Mouse Tumor Biology Database (MTB) Tumor search form.

  WebRENI The primary goal of WebRENI is to provide access to the standardized and internationally harmonized nomenclature and diagnostic criteria of proliferative lesions in rats and mice.

  MPATH: The Pathbase mouse pathology ontology provides a description of mutant and transgenic mouse pathology phenotypes and incorporates 425 known mouse pathologies hierarchically organised as "instances of" pathological processes.

  RENI: Guides for organ sampling and trimming procedures in rats (covers rats, mice)

• Plasmodium:
  Parasite Life-cycle ontologies: This is a temporary website will be used as a place to for displaying new parasite life cycle ontologies terms.

• Rat (taxon-rattus):
  Histobank: The interactive histology atlas.

  UNSW Embryology Rat Development The University of New South Wales Embryology Resource developed for Revision of concepts in embryological development.

  WebRENI The primary goal of WebRENI is to provide access to the standardized and internationally harmonized nomenclature and diagnostic criteria of proliferative lesions in rats and mice.

  RENI: Guides for organ sampling and trimming procedures in rats

• Rice:
  Gramene: Controlled Vocabulary and Ontology for Plants.

• Zebrafish:
  ZFIN: The Zebrafish Information Network.

• General:
  ATCC: American Type Culture Collection. Collections and Repository:All collections.

  CABRI: Common Access to Biological Resources and Information. Data input & authentication.

  ChemIDplus: A database of 350,000 chemical records, including over 100,000 with structures. Locator links allow immediate searching of other databases for information about a given chemical.

  GOBO: Global open biological ontologies.

  Gramene plant trait ontology.

  HistoBank: The interactive histology atlas. (covers human, mouse, rat)

  ILAR: The Institute for Laboratory Animal Research. Animal Models and Genetic Stocks Information Program.

  LOINC:The purpose of the LOINC database is to facilitate the exchange and pooling of results, such as blood hemoglobin, serum potassium, or vital signs, for clinical care, outcomes management, and research.

  Medical Subject Headings (MeSH): The Medical Subject Headings comprise NLM's controlled vocabulary used for indexing articles, for cataloging books and other holdings, and for searching MeSH-indexed databases, including MEDLINE. MeSH terminology provides a consistent way to retrieve information that may use different terminology for the same concepts. MeSH is a principal component vocabulary of the Unified Medical Language System (UMLS®). [listed below]

  Taxonomy Browser: The NCBI Taxonomy Homepage.

  Unified Medical Language System (UMLS): NLM's Unified Medical Language System (UMLS) project develops and distributes multi-purpose, electronic "Knowledge Sources" and associated lexical programs. System developers can use the UMLS products to enhance their applications -- in systems focused on patient data, digital libraries, Web and bibliographic retrieval, natural language processing, and decision support. Researchers will find the UMLS products useful in investigating knowledge representation and retrieval questions.

• Organism:
  Definition: The genus and species (and subspecies) of the organism from which the BioMaterial is derived from.

  Sources: Taxonomy Browser:

• Cell source:
  Definition: The resource (e.g, company, hospital, geographical location) used to obtain or purchase the BioMaterial and the type of specimen.

  Sources: The mailing address can be used for resources that can be contacted. For resources that cannot be contacted such as geographical areas, recommendations for information to be provided are longitude and latitude or map locations and the identity of the map.

• Cell type:
  Defintion: Cell type used in the experiment if non mixed. If mixed the targeted cell type should be used.

  Sources:
  C. Elegans Parts Index
  CBIL's controlled vocabularies
  EMAP
  FlyBase: GOBO version
  The IUPS Physiome Project
  The Mouse Anatomical Dictionary
  TAIR anatomy terms and definitions. Also see GOBO version.
  ZFIN Zebrafish anatomical dictionary.
  WormBase Pedigree Browser
  

• Sex:
  Definition: Term applied to any organism able to undergo sexual reproduction in order to differentiate the individuals or type involved. Sexual reproduction is defined as the ability to exchange genetic material with the potential of recombinant progeny.

  Source: MGED Ontology
  

  Gender	Definition
  male	The organism contains only the reproductive organ that produces male gametes (spermatozoa).
  female	The organism contains only the reproductive organs that produces female gametes (oocytes).
  hermaphrodite	The organism contains both male and female reproductive organs.
  mixed sex	Both male and femal organisms are included.
  unknown sex	The reproductive organs of the organism are unknown.

• Age:
  Definition: The time period elapsed since an identifiable point in the life cycle of an organism. (If a developmental stage is specified, the identifiable point would be the beginning of that stage. Otherwise the identifiable point must be specified such as planting).

  Source: MGED ontology
  

  Initial time point	Definition
  beginning of stage	The time point is the beginning of the specified developmental stage.
  birth	The time point at the end of parturition.
  coitus	The time point at which the organisms have mated.
  planting	The time point at which a seed is planted.

• Developmental stage:
  Definition: The developmental stage of the organism's life cycle during which the BioMaterial was extracted.

  Sources:
  AFGC:
  Cytomer
  UNSW Embryology Chicken Development
  Edinburgh Mouse Atlas
  EMAP
  FlyBase: GOBO version
  Human Developmental Anatomy:
  The Mouse Anatomical Dictionary:
  UNSW Embryology Rat Development
  Parasite Life-cycle ontologies
  TAIR developmental stage terms and definitions. See also GOBO version.
  WormBase: GOBO version
  ZFIN: Stages of embryonic development of the zebrafish.

• Organism part:
  Definition: The part of the organism's anatomy from which the BioMaterial was derived.

  Sources:
  AFGC
  CBIL's Controlled Vocabularies
  UNSW Embryology Chicken Development
  Cytomer
  EMAP
  FlyBase: GOBO version
  GALEN
  Histobank
  Human Developmental Anatomy
  IUPS Physiome Project
  The Mouse Anatomical Dictionary
  Systematized Nomenclature of Medicine (SNOMED):
  TAIR: GOBO version
  UNSW Embryology Rat Development
  WebRENI
  ZFIN

• Strain or line:
  Definition: Animals or plants that have a single ancestral breeding pair or parent as a result of brother x sister or parent x offspring matings.

  Sources:
  ATCC
  International Committe on Standard Genetic Nomenclature for Mice. see also MGI 2.7 - Strains and Polymorphisms Menu.
  ILAR
  ZFIN
  

• Genetic Variation:
  Definition: The genetic modification introduced into the organism from which the BioMaterial was derived. Examples of genetic variation include specification of a transgene or the gene knocked-out.

  Sources:
  ABRC
  AFGC
  TAIR
  International Committe on Standard Genetic Nomenclature for Mice
  FlyBase
  

• Individual number:
  Definition: Identifier or number of the individual organism from which the BioMaterial was derived. For patients, the identifier must be approved by Institutional Review Boards (IRB, review and monitor biomedical research involving human subjects) or appropriate body.

  Sources: This will be a number or ID.
  

• Individual genetic characteristics:
  Definition: The genotype of the individual organism from which the BioMaterial was derived.

  Sources:
  AFGC
  TAIR
  International Committe on Standard Genetic Nomenclature for Mice. see also Mouse nomenclature rules and guidelines or Names and Symbols for Mutant Alleles.
  

• Disease state:
  Definition: The name of the pathology diagnosed in the organism from which the BioMaterial was derived. The disease state is normal if no disease has been diagnosed.

  Sources:
  GALEN
  ICD-9-CM
  MTD
  NTP code tables
  MPATH
  SNOMED
  UMLS
  WebRENI
  

• Targeted cell type:
  Definition: The targeted cell type is the cell of primary interest. The BioMaterial may be derived from a mixed population of cells although only one cell type is of interest.

  Sources:
  C. Elegans Parts Index CBIL's controlled vocabularies
  EMAP
  FlyBase
  IUPS Physiome Project
  The Mouse Anatomical Dictionary
  TAIR anatomy terms and definitions.
  ZFIN Zebrafish anatomical dictionary.
  WormBase Pedigree Browser
  

• Cell line:
  Definition: The identifier for the immortalized cell line if one was used to derive the BioMaterial.

  Sources:
  ATCC
  CABRI
  

• Clinical Information:
  Definition: Clinical information distinct from the disease state that can be referred to from an established controlled vocabulary or ontology. An example might be a test performed and/or finding.

  Sources:
  LOINC:The purpose of the LOINC database is to facilitate the exchange and pooling of results, such as blood hemoglobin, serum potassium, or vital signs, for clinical care, outcomes management, and research.
  National Toxicology Program. Clinical measurements.

• PhysicalCharacteristics:
  Definition: Phenotype and traits not including pathology and disease.

  Sources: Gramene

Enzyme Nomenclature: Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB).

Gene OntologyTM Consortium: The Gene Ontology (GO) Consortium is generating ontologies for molecular function, biological process, and cellular component. This effort represents knowledge domains that are important to interpreting microarray results. The GO consortium includes groups working on Drosophila, Saccharomyces, Mus, Arabidopsis, and Caenorhabditis.

KEGG: Kyoto Encyclopedia of Genes and Genomes. Table of Contents.

WIT: What Is There? Interactive Metabolic Reconstruction on the WEB.