Species specific ontology resources available:
- 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 SNOMEDŽ. 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.
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