1.3
TC
Transport Classification Database
The TC-DB website details a comprehensive classification system for membrane transport
proteins known as the Transport Classification (TC) system. -- http://megaman.ucsd.edu/tcdb
ENSEMBL
Ensembl project
The Ensembl project produces genome databases for vertebrates and other eukaryotic species,
and makes this information freely available online. - http://www.ensembl.org
EC
Enzyme Nomenclature
SwissProt Enzyme nomenclature database ENZYME is a repository of information relative to
the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature
Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes
each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided. -
http://www.expasy.ch/enzyme/
UMBBD
University of Minnesota Biocatalysis/Biodegradation Database
This database contains information on microbial biocatalytic reactions and biodegradation
pathways for primarily xenobiotic, chemical compounds. - http://umbbd.msi.umn.edu
BROAD
Broad Institute
Broad Institute of MIT and Harvard - http://www.broad.mit.edu
UWASH
University of Washington Multimegabase Sequencing Center
Washington University School of Medicine in St. Louis -
http://www.genome.washington.edu/uwgc/
EO
Environment Ontology
A set of standardized controlled vocabularies to describe various types of treatments given
to a individual plant / a population or a cultured tissue and/or cell type sample to evaluate the
response on its exposure. It also includes the study types, where the terms can be used to identify
the growth study facility. Each growth facility such as field study, growth chamber, green house etc
is a environment on its own it may also involve instances of biotic and abiotic environments as
supplemental treatments used in these studies. -
http://www.gramene.org/plant_ontology/ontology_browse.html
UMan
University of Manchester
Britain's largest single-site university with a proud history of achievement and an
ambitious agenda for the future. - http://www.manchester.ac.uk/
NC_NP
NCBI protein sequence database
NCBI protein sequence from REFSEQ (National Center for Biotechnology Information) -
http://www.ncbi.nlm.nih.gov/RefSeq/
NC_NM
NCBI DNA/RNA sequence database
NCBI DNA/RNA sequence from REFSEQ (National Center for Biotechnology Information) -
http://www.ncbi.nlm.nih.gov/RefSeq/
ECOCYC
EcoCyc
Database that describes the genome and the biochemical machinery of E. coli, maintained by
SRI International, Menlo Park, CA. - http://www.ecocyc.org
PROSITE
ExPASy Proteomics Server
PROSITE consists of documentation entries describing protein domains, families and
functional sites as well as associated patterns and profiles to identify them. -
http://www.expasy.ch/prosite
GR
Gramene
A Resource for Comparative Grass Genomics - http://www.gramene.org/
GO
Gene Ontology
The Gene Ontology project is a major bioinformatics initiative with the aim of
standardizing the representation of gene and gene product attributes across species and databases. -
http://www.geneontology.org/
SMART
Simple Modular Architecture Research Tool
SMART (a Simple Modular Architecture Research Tool) allows the identification and
annotation of genetically mobile domains and the analysis of domain architectures. More than 500
domain families found in signalling, extracellular and chromatin-associated proteins are detectable.
- http://smart.embl-heidelberg.de/
PATHODB
BIOBASE PathoDB
PathoDB is a database on pathologically relevant mutated forms of transcription factors and
their binding sites. - http://www.biobase-international.com/index.php?id=pathodb
KAZUSA
Kazusa DNA Research Institute
Japanese Genetics Institute - http://www.kazusa.or.jp
AC
AraCyc
AraCyc is a metabolic pathway database for Arabidopsis thaliana that contains information
about both predicted and experimentally determined pathways, reactions, compounds, genes and
enzymes. - http://www.arabidopsis.org/biocyc/
HOMSTRAD
HOMologous STRucture Alignment Database
HOMSTRAD (HOMologous STRucture Alignment Database) is a curated database of structure-based
alignments for homologous protein families. - http://tardis.nibio.go.jp/homstrad
RSNP
Repository of Single Nucleotide Polymorphism
A system of databases documenting the influence of mutations in regulatory gene regions
onto DNA interaction with nuclear proteins. - http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp
CL
Cell Ontology
The Cell Ontology is designed as a structured controlled vocabulary for cell types. -
http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell
TRANSCOMPEL
TRANSCompel
Composite regulatory elements are found in many promoters and enhancers of eukaryotic
genes. They consist of two binding sites of two different transcription factors, which through this
combination form a module with new regulatory properties. Composite elements frequently serve as
integration sites of two (or more) signaling pathways. -
http://www.biobase-international.com/pages/index.php?id=transcompel
MC
MetaCyc
MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways.
MetaCyc contains more than 1400 pathways from more than 1800 different organisms, and is curated
from the scientific experimental literature. - http://metacyc.org/
PHYTOZOME
Phytozome
Phytozome is a joint project of the Department of Energy's Joint Genome Institute and the
Center for Integrative Genomics to facilitate comparative genomic studies amongst green plants. -
http://www.phytozome.net
PHYTOZOME-POPLAR
Phytozome Poplar DB
Poplar specific data on Phytozome which is a joint project of the Department of Energy's Joint Genome Institute and the
Center for Integrative Genomics to facilitate comparative genomic studies amongst green plants. -
http://www.phytozome.net
MGI
Mouse Genome Informatics
MGI: the international database resource for the laboratory mouse, providing integrated
genetic, genomic, and biological data for researching human health. -
http://www.informatics.jax.org/
GOAEBI
Gene Ontology Annotation
The GOA project aims to provide high-quality Gene Ontology (GO) annotations to proteins in
the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI) and is a central dataset
for other major multi-species databases; such as Ensembl and NCBI. - http://www.ebi.ac.uk/GOA/
MIRBASE
miRBase - the microRNA database
The miRBase database is a searchable database of published miRNA sequences and annotation.
Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA
transcript (termed mir in the database), with information on the location and sequence of the mature
miRNA sequence (termed miR). - http://microrna.sanger.ac.uk
unknown
unknown data source
When the data source is unknown, e.g. data parsed from excel spreadsheets not part of a
particular database or consortium.
PO
Plant Ontology
Ontologie that describe plant structures and growth
and developmental stages, providing a semantic
framework for meaningful cross-species queries
across databases. http://www.plantontology.org/
NEWT
UniProt Taxonomy Database
NEWT is the taxonomy database maintained by the UniProt group. It integrates taxonomy data
compiled in the NCBI database and data specific to the UniProt Knowledgebase. -
http://www.uniprot.org/help/taxonomy
CAS
Chemical Abstracts Service
CAS offers the CAS REGISTRYSM - the largest collection of substance information - as well
as indexed references from more than 10,000 major scientific journals and 59 patent authorities
around the world. - http://www.cas.org/
GENEDB
GeneDB
The GeneDB project is a core part of the Sanger Institute Pathogen Sequencing Unit's (PSU)
activities. - http://www.genedb.org/
RESID
RESID - Database of Protein Modifications
The RESID Database of Protein Modifications is a comprehensive collection of annotations
and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide
chain cross-link post-translational modifications. - http://www.ebi.ac.uk/RESID/
IAH
Institute for Ageing and Health
Institute for Ageing and Health, Newcastle University - http://www.ncl.ac.uk/iah/
CCSD
Complex Carbohydrate Structure Database
The Complex Carbohydrate Structure Database (CCSD) and CarbBank, an IBM PC/AT (or
compatible) database management system, were created to provide an information system to meet the
needs of people interested in carbohydrate science. -
http://www.boc.chem.uu.nl/sugabase/carbbank.html
VO
Virtual Ontology
Virtual Ontology, a temporary ontology with no permanent representation outside ONDEX.
CAMJE
CAMJE
Campylobacter jejuni proteome - http://www.expasy.ch/sprot/hamap/CAMJE.html
UC
unclassified data source
The data source cannot be classified. This is for example the case for concepts merged
together from different CVs.
INTACT
IntAct
IntAct provides a freely available, open source database system and analysis tools for
protein interaction data. All interactions are derived from literature curation or direct user
submissions and are freely available. - http://www.ebi.ac.uk/intact
PROID
DDBJ/EMBL-bank/GenBank databases
The protein identifier shared by DDBJ/EMBL-bank/GenBank nucleotide (e.g. CAA71991)
TIGR
The Institute for Genomic Research
The Institute for Genomic Research (TIGR) was a non-profit genomics research institute
founded in 1992 by Craig Venter in Rockville, Maryland, United States. It is now a part of the J.
Craig Venter Institute. - http://www.tigr.org
REAC
Reactome
A curated knowledgebase of biological pathways. - http://www.reactome.org
WN
WordNet
WordNet is a large lexical database of English, developed under the direction of George A.
Miller. Nouns, verbs, adjectives and adverbs are grouped into sets of cognitive synonyms (synsets),
each expressing a distinct concept. - http://wordnet.princeton.edu/
WB
WormBase
WormBase is an international consortium of biologists and computer scientists dedicated to
providing the research community with accurate, current, accessible information concerning the
genetics, genomics and biology of C. elegans and some related nematodes. - http://www.wormbase.org
GeneRIF
Gene Reference Into Function
GeneRIF provides a simple mechanism to allow scientists to add to the functional annotation
of genes described in Entrez Gene. - http://www.ncbi.nlm.nih.gov/projects/GeneRIF
TAIR
The Arabidopsis Information Resource
The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular
biology data for the model higher plant Arabidopsis thaliana. - http://www.arabidopsis.org/
HSSP
Homology-derived Secondary Structure of Proteins
The HSSP database is a database of homology-derived secondary structure of proteins. -
http://swift.cmbi.kun.nl/gv/hssp/
BRENDA
Enzyme Database - BRENDA
The Comprehensive Enzyme Information System - http://www.brenda-enzymes.org/
TF
TRANSFAC
BIOBASE TRANSFAC Professional: The most comprehensive collection of eukaryotic gene
regulation data - http://www.biobase-international.com/pages/index.php?id=transfac
AHD
Arabidopsis Hormone Database
Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database
for plant hormone research in Arabidopsis - Peng et al., Nucleic Acids Research 2009 37(Database
issue):D975-D982; doi:10.1093/nar/gkn873
PFAM
Pfam
Pfam is a large collection of multiple sequence alignments and hidden Markov models
covering many common protein domains and families. - http://pfam.sanger.ac.uk/
TO
Trait Ontology
It is a controlled vocabulary to describe each trait as a distinguishable feature,
characteristic, quality or phenotypic feature of a developing or mature individual. Examples are
glutinous endosperm, disease resistance, plant height, photosensitivity, male sterility, etc. -
http://www.gramene.org/plant_ontology/ontology_browse.html#to
TP
TRANSPATH
BIOBASE Transpath Database: TRANSPATH is a database system about gene regulatory networks
that combines encyclopedic information on signal transduction with tools for visualization and
analysis. - http://www.biobase.de/
SO
Sequence Ontology
The Sequence Ontology is a set of terms and relationships used to describe the features and
attributes of biological sequence. - http://www.sequenceontology.org/
OMIM
Online Mendelian Inheritance in Man
OMIM, Online Mendelian Inheritance in Man, a database of human genes and genetic disorders
developed by staff at Johns Hopkins and hosted on the Web. - http://www.ncbi.nlm.nih.gov/omim
SA
Sanger Institute
The Sanger Institute is a genome research institute primarily funded by the Wellcome Trust.
- http://www.sanger.ac.uk/
VEGA
The Vertebrate Genome Annotation database
The Vertebrate Genome Annotation (VEGA) database is a central repository for high quality
manual annotation of vertebrate finished genome sequence. - http://vega.sanger.ac.uk
BKL
BIOBASE Knowledge Library
With content covering disease, drugs, gene regulation, pathways, and fully annotated
genomes. - http://www.biobase-international.com/index.php?id=databasesandtools
NITE
National Institute for Technology and Evaluation
National Institute for Technology and Evaluation - http://www.nite.go.jp/index-e.html
UM-P
UM-P
UM-BBD_pathwayID
UM-E
UM-E
UM-BBD_enzymeID
maizeGDB
Maize Genetics and Genomics Database
MaizeGDB is the community database for biological information about the crop plant Zea mays
ssp. mays. Genetic, genomic, sequence, gene product, functional characterization, literature
reference, and person/organization contact information are among the datatypes accessible through
this site. - http://www.maizegdb.org/
PRINTS
Protein fingerprints
A compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to
characterise a protein family; its diagnostic power is refined by iterative scanning of a
SWISS-PROT/TrEMBL composite. - http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS
ATREGNET
AtRegNet
AtRegNet is a tool used to display the regulatory networks of Arabidopsis thaliana
transcription factors. - http://arabidopsis.med.ohio-state.edu/moreNetwork.html
ENCODE
ENCyclopedia Of DNA Elements
The National Human Genome Research Institute (NHGRI) launched a public research consortium
named ENCODE, the Encyclopedia Of DNA Elements, in September 2003, to carry out a project to
identify all functional elements in the human genome sequence. - http://www.genome.gov/10005107
DOI
Digital Object Identifier
The Digital Object Identifier (DOI ) System is for identifying content objects in the
digital environment. - http://www.doi.org/
FLYBASE
FlyBase
A Database of Drosophila Genes and Genomes - http://flybase.org/
UNIGENE
UniGene - An Organized View of the Transcriptome
Each UniGene entry is a set of transcript sequences that appear to come from the same
transcription locus (gene or expressed pseudogene), together with information on protein
similarities, gene expression, cDNA clone reagents, and genomic location. -
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene
HGNC
HUGO Gene Nomenclature Committee
Gene Nomenclature Committee HUGO symbols - Giving unique and meaningful names to every
human gene. - http://www.genenames.org/
Oryzabase
Oryzabase
The Oryzabase is a comprehensive rice science database established in 2000 by rice
researcher's committee in Japan. The database is originally aimed to gather as much knowledge as
possible ranging from classical rice genetics to recent genomics and from fundamental information to
hot topics. - http://www.shigen.nig.ac.jp/rice/oryzabase/top/top.jsp
DRA
Drastic Insight Database
Drastic: A Database Resource for the Analysis of Signal Transduction In Cells -
http://www.drastic.org.uk
PubMed
PubMed
PubMed comprises more than 19 million citations for biomedical articles from MEDLINE and
life science journals. Citations may include links to full-text articles from PubMed Central or
publisher web sites. - http://www.ncbi.nlm.nih.gov/pubmed/
TRANSPRO
TRANSPro
Promoter sequences are defined according to the annotated transcription start sites (TSS),
which are retrieved and clustered by a proprietary algorithm to distinguish alternative promoters of
individual genes. TRANSPro is a necessary resource for systematic promoter analysis of co-regulated
genes. Known transcription factor binding sites are indicated. -
http://www.biobase-international.com/index.php?id=transpro
SCOP
Structural Classification of Proteins
The SCOP database, created by manual inspection and abetted by a battery of automated
methods, aims to provide a detailed and comprehensive description of the structural and evolutionary
relationships between all proteins whose structure is known. - http://scop.mrc-lmb.cam.ac.uk/scop/
MENDEL
Mendel - plant gene nomenclature
The Mendel database contains names for plant-wide families of sequenced plant genes for
Commission on Plant Gene Nomenclature (CPGN). - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC29857/
MEROPS
MEROPS
The MEROPS database is an information resource for peptidases (also termed proteases,
proteinases and proteolytic enzymes) and the proteins that inhibit them. -
http://merops.sanger.ac.uk/
3DMET
3DMET
A three-dimensional-structure database of natural metabolites 3DMET is a database
collecting three-dimensional structures of natural metabolites - http://www.3dmet.dna.affrc.go.jp/
PIR
Protein Information Resource
The Protein Information Resource (PIR) is an integrated public bioinformatics resource to
support genomic, proteomic and systems biology research and scientific studies. -
http://pir.georgetown.edu
UNIPARC
UniParc
UniProt Archive (UniParc) is part of UniProt project. It is a non-redundant archive of
protein sequences extracted from public databases UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, PIR-PSD,
EMBL, EMBL WGS, Ensembl, IPI, PDB, PIR-PSD, RefSeq, FlyBase, WormBase, H-Invitational Database,
TROME database, European Patent Office proteins, United States Patent and Trademark Office proteins
(USPTO) and Japan Patent Office proteins. - http://www.ebi.ac.uk/uniparc/
CAZY
Carbohydrate-Active enZymes
The CAZy database describes the families of structurally-related catalytic and
carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create
glycosidic bonds. - http://www.cazy.org/
PSI-MIO
PSI-MI Ontology
Proteomics Standards Initiative - Molecular Interactions Ontology. -
http://www.psidev.info/
SMOD
SWISS-MODEL
SWISS-MODEL is a fully automated protein structure homology-modeling server, accessible via
the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer). -
http://swissmodel.expasy.org/
PHI
PHI-base
Pathogen - Host Interaction database - http://www.phibase.org
HUGE
Human Unidentified Gene-Encoded
The HUGE protein database has been created to publicize the fruits of our Human cDNA
project at the Kazusa DNA Research Institute. - http://www.kazusa.or.jp/huge/
HINVDB
H-InvDB
H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts.
- http://hinvdb.ddbj.nig.ac.jp/ahg-db/index.jsp
RGD
Rat Genome Database
The Rat Genome Database is a collaborative effort between leading research institutions
involved in rat genetic and genomic research. - http://rgd.mcw.edu/
RATMAP
The Rat Genome Database. RATMAP
The Rat Genome Database RatMap is focused on presenting rat genes, DNA-markers,
QTL:s etc that is localized to chromosome. - http://ratmap.gen.gu.se/
IPRO
InterPro
A database of protein families, domains and functional sites in which identifiable features
found in known proteins can be applied to unknown protein sequences. - http://www.ebi.ac.uk/interpro
MSDchem
Macromolecular Structure Database Group
MSDchem: Consistent and enriched library of ligands, small molecules and monomers that are
referred as residues and hetgroups in any PDB entry. - http://www.ebi.ac.uk/msd-srv/msdchem
JGI
Joint Genome Institute
The U.S. Department of Energy Joint Genome Institute, supported by the DOE Office of
Science, unites the expertise of five national laboratories - Lawrence Berkeley, Lawrence Livermore,
Los Alamos, Oak Ridge, and Pacific Northwest - along with the HudsonAlpha Institute for
Biotechnology to advance genomics in support of the DOE missions related to clean energy generation
and environmental characterization and cleanup. - http://www.jgi.doe.gov/
Poplar-JGI
Poplar DB at JGI
Poplar database at JGI which is the U.S. Department of Energy Joint Genome Institute,
- http://www.jgi.doe.gov/
MODBASE
Database of Comparative Protein Structure Models
MODBASE is a queryable database of annotated protein structure models. -
http://modbase.compbio.ucsf.edu
NCBI
National Center for Biotechnology Information
National Center for Biotechnology Information, National Library of Medicine, National
Institutes of Health. - http://www.ncbi.nlm.nih.gov/
NCI
NCI Chemical Carcinogen Repository
The National Cancer Institute (NCI) contracts with MRI to operate a repository that
supplies standard reference-grade compounds for cancer research. -
http://www.mriresearch.org/WorkingWithMRI/NCIRepository.asp
EMBL
EMBL-EBI International Nucleotide Sequence Data
The EMBL Nucleotide Sequence Database (also known as EMBL-Bank) constitutes Europe's
primary nucleotide sequence resource. - http://www.ebi.ac.uk/embl/
KEGG
Kyoto Encyclopedia of Genes and Genomes
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a bioinformatics resource for linking
genomes to life and the environment. - http://www.genome.jp/kegg/
SMARTDB
S/MAR transaction DataBase
S/MARt DB collects information about scaffold/matrix attached regions and the nuclear
matrix proteins that are supposed be involved in the interaction of these elements with the nuclear
matrix. - http://smartdb.bioinf.med.uni-goettingen.de
PDB
Protein Data Bank
A Resource for Studying Biological Macromolecules - The PDB archive contains information
about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. -
http://www.pdb.org
AFFYMETRIX
Affymetrix
A pioneer in genetic analysis, Affymetrix introduced highly parallel genetic assays to the
marketplace by commercializing the first DNA microarray in the late 1980s. -
http://www.affymetrix.com
WIKI
Wikipedia
Wikipedia, the free encyclopedia that anyone can edit. - http://wikipedia.org
AFCS
AfCS
Alliance for Cellular Signaling - http://www.afcs.org/
GrainGenes
GrainGenes
A database for Triticeae and Avena - http://wheat.pw.usda.gov/GG2/index.shtml
EPD
Eukaryotic Promoter Database
The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL
II promoters, for which the transcription start site has been determined experimentally. -
http://www.epd.isb-sib.ch
PUBCHEM
PubChem
Free database of chemical structures of small organic molecules and information on their
biological activities. - http://pubchem.ncbi.nlm.nih.gov/
BIOGRID
BioGRID
General Repository for Interaction Datasets - http://thebiogrid.org
dbEST
dbEST
dbEST (Nature Genetics 4:332-3;1993) is a division of GenBank that contains sequence data
and other information on "single-pass" cDNA sequences, or Expressed Sequence Tags, from a number of
organisms. - http://www.ncbi.nlm.nih.gov/dbEST/
LYCOCYC
LycoCyc
Developed by the Solanaceae Genomics Network, LycoCyc is a catalog of known and/or
predicted biochemical pathways from tomato (Solanum lycopersicum). -
http://pathway-dev.gramene.org/gramene/lycocyc.shtml
SGN
Sol Genomics Network
http://solgenomics.net
GENB
GenBank
GenBank Nucleic Acid Sequence Database - http://www.ncbi.nlm.nih.gov/Genbank/
SGD
Saccharomyces Genome Database
SGD is a scientific database of the molecular biology and genetics of the yeast
Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast. -
http://www.yeastgenome.org/
NLM
National Library Of Medicine
The Library collects materials and provides information and research services in all areas
of biomedicine and health care. - http://www.nlm.nih.gov/
EMBLC
EMBL-EBI International Nucleotide Sequence Data Clones
The EMBL Nucleotide Sequence Database (also known as EMBL-Bank) constitutes Europe's
primary nucleotide sequence resource. - http://www.ebi.ac.uk/embl/
MIPS
Munich Information Center for Protein Sequences
The Munich Information Center for Protein Sequences (MIPS) is a research center hosted at
the Institute for Bioinformatics (IBI) at Neuherberg, Germany with a focus on genome oriented
bioinformatics, in particular on the systematic analysis of genome information including the
development and application of bioinformatics methods in genome annotation, gene expression analysis
and proteomics. - http://mips.gsf.de/
NC_GE
NCBI GE GeneID database
These GeneID values are specific for the ENTREZGENE database at the National Center for
Biotechnology Information (THIS IS ABSOLUTELY NOT THE SAME AS: NC_GI) -
http://www.ncbi.nlm.nih.gov/gene
NC_GI
NCBI GI GeneID database
National Center for Biotechnology Information Gene ID -
http://www.ncbi.nlm.nih.gov/entrez/query/static/help/genefaq.html
COG
Clusters of Orthologous Groups of proteins
Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein
sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists
of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an
ancient conserved domain. - http://www.ncbi.nlm.nih.gov/COG/
CHEBI
Chemical Entities of Biological Interest
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of
molecular entities focused on small chemical compounds. - http://www.ebi.ac.uk/chebi/
UNIPROTKB
UniProtKB
UniProtKB is protein sequence database consisting oftwo sections
1. Swiss-Prot, which is manually annotated and reviewed;
2. TrEMBL, which is automatically annotated and not reviewed
- http://www.uniprot.org/
UNIPROTKB-TrEMBL
UniProtKB/TrEMBL
UniProtKB/TrEMBL is a computer-annotated and
not reviewed protein sequence database. - http://www.uniprot.org/
UNIPROTKB-SwissProt
UniProtKB/Swiss-Prot
UniProtKB/Swiss-Prot is a reviewed and manually-annotated
protein sequence database. - http://www.uniprot.org/
TRRD
Transcription Regulatory Regions Database
TRRD is a unique information resource, accumulating information on structural and
functional organization of transcription regulatory regions of eukaryotic genes. Only experimentally
confirmed information is included into TRRD. - http://wwwmgs.bionet.nsc.ru/mgs/gnw/trrd
PlnTFDB
Plant TFDB
Plant Transcription factor databasePlnTFDB (2.0) is a public database arising from efforts
to identify and catalogue all Plant genes involved in transcriptional control. -
http://plntfdb.bio.uni-potsdam.de/v2.0/
KNApSAcK
KNApSAcK
KNApSAcK: A Comprehensive Species-Metabolite Relationship Database. -
http://kanaya.naist.jp/KNApSAcK/
ZFIN
The Zebrafish Information Network
ZIRC is the Zebrafish International Resource Center, an independent NIH-funded facility
providing a wide range of zebrafish lines, probes and health services. - http://zfin.org
PRODOM
ProDom
ProDom is a comprehensive set of protein domain families automatically generated from the
SWISS-PROT and TrEMBL sequence databases. - http://prodom.prabi.fr/prodom/current/html/home.php
CSD
Complex Carbohydrate Research Center
The Complex Carbohydrate Research Center (CCRC) was founded at the University of Georgia
(UGA) in September 1985 to answer the national need for a center devoted to increasing knowledge of
the structures and functions of complex carbohydrates. - http://www.ccrc.uga.edu/
CGSW
Catalogue of Gene Symbols for Wheat
A Catalogue as distributed on the MacGene CD at the 10th International Wheat Genetics
Symposium. - http://wheat.pw.usda.gov/ggpages/wgc/2003/
PLANTCYC
Plant Metabolic Pathway Database
PlantCyc provides access to manually curated or reviewed information about shared and
unique metabolic pathways present in over 250 plant species. - http://www.plantcyc.org/
IRGSP
International Rice Genome Sequencing Project
The International Rice Genome Sequencing Project (IRGSP), a consortium of publicly funded
laboratories, was established in 1997 to obtain a high quality, map-based sequence of the rice
genome using the cultivar Nipponbare of Oryza sativa ssp. japonica. It is currently comprised of ten
members: Japan, the United States of America, China, Taiwan, Korea, India, Thailand, France, Brazil,
and the United Kingdom. The IRGSP adopts the clone-by-clone shotgun sequencing strategy so that each
sequenced clone can be associated with a specific position on the genetic map and adheres to the
policy of immediate release of the sequence data to the public domain. In December 2004, the IRGSP
completed the sequencing of the rice genome. The high-quality and map-based sequence of the entire
genome is now available in public databases. - http://rgp.dna.affrc.go.jp/IRGSP/
IPI
International Protein Index
IPI provides a top level guide to the main databases that describe the proteomes of higher
eukaryotic organisms. - http://www.ebi.ac.uk/IPI
CYORF
Cyanobacteria Gene Annotation Database
CYORF is a vehicle by which the community of cyanobacteriologists collectively annotates
available genomes from cyanobacteria. - http://cyano.genome.jp/
DATF
The Database of Arabidopsis Transcription Factors
The Database of Arabidopsis Transcription Factors (DATF) collects all arabidopsis
transcription factors (totally 1922 Loci; 2290 Gene Models) and classifies them into 64 families. -
http://datf.cbi.pku.edu.cn
DPTF
The Database of Poplar Transcription Factors
The Database of Poplar Transcription Factors (DPTF) collects all poplar
transcription factors (totally 2576 TF) and classifies them into 64 families. -
http://dptf.cbi.pku.edu.cn
MINT
Molecular INTeraction database
MINT focuses on experimentally verified protein-protein interactions mined from the
scientific literature by expert curators. - http://mint.bio.uniroma2.it/mint/
Corpus
Corpus
Set of publications to be analysed
LIPIDMAPS
Lipidomics Gateway
Lipidomics Gateway: a free, comprehensive website for researchers interested in lipid biology. - http://www.lipidmaps.org/
LIPIDBANK
LipidBank
The official database of Japanese Conference on the Biochemistry of Lipids (JCBL). - http://lipidbank.jp/
JCGGDB
Japan Consortium for Glycobiology and Glycotechnology DataBase
Large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc. - http://jcggdb.jp/index_en.html
NIKKAJI
Japan Chemical Substance Dictionary
An organic compound dictionary database prepared by the Japan Science and Technology Agency (JST). - http://nikkajiweb.jst.go.jp/nikkaji_web/pages/top_e.html
HPRD
Human Protein Reference Database
The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. - http://www.hprd.org/
IMGT
ImMunoGeneTics Database
IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. - http://www.ebi.ac.uk/imgt/
DRUGBANK
DrugBank
The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. - http://www.drugbank.ca/
LIGANDBOX
LIGANds Data Base Open and eXtensible
LigandBox (Ligand Data Base Open and eXtensible), a database of small chemical compounds, has been developed by Japan Biological Informatics Consortium (JBIC) as one component of the molecular simulation system, myPresto, in "Structural Proteomics Project" commissioned by the government of Japan. - http://presto.protein.osaka-u.ac.jp/LigandBox/
MeSH
Medline Subject Headings
MeSH is the National Library of Medicine's controlled vocabulary thesaurus. It consists of
sets of terms naming descriptors in a hierarchical structure that permits searching at various
levels of specificity. - http://www.nlm.nih.gov/mesh/
UMLS
Unified Medical Language Systems
The purpose of NLM's Unified Medical Language System (UMLS®) is to facilitate the
development of computer systems that behave as if they "understand" the meaning of the language of
biomedicine and health. To that end, NLM produces and distributes the UMLS Knowledge Sources
(databases) and associated software tools (programs) for use by system developers in building or
enhancing electronic information systems that create, process, retrieve, integrate, and/or aggregate
biomedical and health data and information, as well as in informatics research. By design, the UMLS
Knowledge Sources are multi-purpose. They are not optimized for particular applications, but can be
applied in systems that perform a range of functions involving one or more types of information,
e.g., patient records, scientific literature, guidelines, public health data. The associated UMLS
software tools assist developers in customizing or using the UMLS Knowledge Sources for particular
purposes. The lexical tools work more effectively in combination with the UMLS Knowledge Sources,
but can also be used independently.
BacilluScope
BacilluScope
BacilluScope Bacillus subtilis genome annotation database.
String
String
String 8 database
DBTBS
Bacillus subtilis Transcription Factor Database
http://dbtbs.hgc.jp/
Predictome
A database of predicted functional associations among genes and proteins
http://predictome.bu.edu
A
ampere
SI BASE Unit of electric current
K
kelvin
SI BASE Unit of temperature
mol/dm-3
mol/(dm^3)
concentration: mol per litre
hour
hour
Non SI time unit
1 hour = 60 minutes = 3600 seconds
s
second
SI BASE Unit of time
day
day
Non SI time unit
1 day = 24 hours
(mol/dm3)1-n/s-1
(mol/dm3)1-n/s-1
units for rate constant of any order
mol/dm3/s-1
mol/(dm^3 * s)
change of concentration
mol per litre and second
cd
candela
SI BASE Unit of light intensity
s-1
s^(-1)
Unit of Frequency (events per second)
second
second
SI Base Unit of time
kg
Kilogramme
SI BASE Unit of weight
1 kg is the weight of 1dm^3 water at 9.81Newton gravitational force
mol
mol
SI BASE Unit indicating the amount of substance
~ 1.6 E 23 molecules
min
minute
Non SI time unit
(1 minute = 60 seconds)
Matrix
Matrix
java.lang.Object
GDS
GDS
General data store
java.lang.Object
Pheno
Phenotype
Phenotype of mutant
java.lang.String
AUTHORS
Authors
Author ";" deliminated
java.lang.String
GO_REF
GO_Reference
it indicats the way the relations was annotated
java.lang.String
description
description
General description
java.lang.String
AA
AminoacidSequence
Any Sequence of Amino Acids like a protein
java.lang.String
BM
BindingMotif
Binding motif
java.lang.String
ACCHITS
ACCHITS
counts of hits for this accession based mapping
java.lang.Integer
PROBSTAT
Probabilistics+Statistics
java.lang.Object
TRAN
Temperature_Range
temperature range value
java.lang.Double
graphical
graphical
coordinates
java.awt.geom.Point2D
ecotype
ecotype
Ecotype
java.lang.String
NA
Nucleic_acid_sequence
Any Sequence of Nuclein Acids like DNA or RNA
java.lang.String
Measurement
Measurement
java.lang.Object
Mr
molecular mass/molecular weight
Previously molecular weight(MW)/ molecular mass(Mr)
is equal to 1/12 the mass of one atom of carbon-12
java.lang.Float
pos_tag
position_tag
part of speech tag
java.lang.String
YEAR
Year published
The year the article was published
java.lang.Integer
ID
Identifier
java.lang.Object
NWBWeight
Network Workbench weight
Custom weight attribute used by network workbench
java.lang.Double
KI
KI-value
KI value
java.lang.Double
KM
KM-value
KM value
java.lang.Double
Score
Score
java.lang.Object
BEGIN
Start of feature
Location of start of a feature
In the case of DNA, taken to be the lowest base pair location from
the forward strand, regardless of sense strand for the feature.
java.lang.Integer
BEV
BindingEvidence
Evidence for binding
java.lang.String
mutagenesis_type
mutagenesis_type
Mutagenesis type
java.lang.String
PVALUE
p-value
The probability of obtaining a value of the test statistic at least as extreme as the one
that was actually observed, given that the null hypothesis is true.
java.lang.Float
CoCitNum
Cooccurrence - #Publications
Number of publications where two concepts are mentioned together
java.lang.Integer
CoSenNum
Cooccurrence - #Sentences
Number of sentences where two concepts are mentioned together
java.lang.Integer
TFIDF
TFIDF
Term frequency - inverse document frequency is a weight often used in information retrieval and
text mining. This weight is a statistical measure used to evaluate how
important a word is to a document in a collection or corpus.
java.lang.Double
IP_TFIDF
Inner product of TFIDF
Inner product of all TFIDF scores
java.lang.Double
MAX_TFIDF
Maximum of TFIDF
Maximum of all TFIDF scores
java.lang.Double
MUTUAL_INF
Mutual information
Mutual information quantifies the dependence between the joint distribution of X and Y and what the joint distribution would be if X and Y were independent.
java.lang.Double
TM_SCORE
text mining score
Score to define quality of text mining based
mappings
java.lang.Double
dominance
dominance
Dominance, co-dominance, or recessive.
java.lang.String
TFM
TFM
Transfac Matrix
java.lang.String
RT
RegulatorType
Regulator Type
java.lang.String
RNAS
RNA-Sequence
RNA Sequence containing Uracil
java.lang.String
INTERNAL
InternalTypes
java.lang.Object
LOGL
log Likelihood
natural logarithm of the likelihood.
java.lang.Double
AbstractHeader
Title
Title of a Publication
java.lang.String
FullText
Full Text
Full text of a Publication
java.lang.String
GENLOC
Genetic_Location
java.lang.Object
THETA
theta value
probability that the nodes, whose lowest common ancestor
this node is, are connected by an edge.
java.lang.Double
SXCONF
StructAlign Confidence
StructAlign Confidence value
java.lang.Integer
Abstract
Abstract
Abstract of a Publication
java.lang.String
CLASS
MetabolicClass
Metabolism classes
java.lang.String
DOI
DOI
Digital Object Identifier
java.lang.String
PFAMHITS
Pfam mapping hits
Number of hits in the pfam-based ortholog prediction
java.lang.Integer
BLEV
BLAST E-Value
The number of different alignents with scores
equivalent to or better than S that are expected to
occur in a database search by chance. The lower the
E value, the more significant the score.
java.lang.Double
TFBSS
TFBS-Sequence
The Sequence that a Transcription Factor Binds To
java.lang.String
EVIDENCE
evidence sentences
evidence text that support the validation of a mapping
java.util.HashSet
CONF
confidence
Confidence value
java.lang.Double
DataSources
Data_Sources
List of data sources. To be used by merging transformations.
java.util.List
gene_role
gene_role
Gene role.
java.lang.String
AFFYCHIPSET
Affymatrix chipset
Unique identifier for an Affymatrix chip
java.lang.String
2SYS
2Syn-mapping_score
Score from 2Syn mapping
java.lang.String
Sequence
Sequence
java.lang.Object
STR
Strand
Strand (+) for forward, (-) for reverse, (S) for sense, (.) for otherwise. (W) for Watson
java.lang.Character
microarray
microarray
Microarray information
java.lang.String
PROANNO
Provisional annotation
A provisional protein annotation
java.lang.String
MeSH
Medical Subject Headings
NLM's controlled vocabulary, used to characterize
the content of MEDLINE citations.
java.lang.String
Chemical
Chemical
Chemical terms associated
to MEDLINE abstracts.
java.lang.String
IMAGE
ImageLink
A url which represents a link to an image.
java.lang.String
DNAS
DNA_sequence
DNA Sequence
java.lang.String
SUBUS
Subunits
sub units
java.lang.String
PUB_TYPE
Type of Publication
Describes the type of the publication as in
the RP line of UniProt entries parse RP line:
http://www.uniprot.org/docs/userman.htm#RP_line
java.lang.String
2Lconf
two level confidence measure
This is a confidence attribute where there are only two values.
i.e. when things are either "confident" or "not confident"
java.lang.Boolean
REG
regulation
regulation
java.lang.Boolean
2SYNHITS
2SYNHITS
counts of hits for this name based mapping
java.lang.Integer
Chromosome
Chromosome
Main linkage groups of the organism
java.lang.Integer
Scaffold
Scaffold
A sequence region which has no physical mapping to one of
the main linkage groups (Chromosomes)
java.lang.Integer
Classification
Classification
java.lang.Object
TAXID
Taxonomy_ID
NCBI Taxonomic Identifier
java.lang.String
JOURNAL_REF
Journal reference for a publication
The Journal reference for a publication
java.lang.String
PWM
PWM
Position Weight Matrix
java.lang.String
mutatedSite
mutatedSite
Details of site of mutation
java.lang.String
BITSCORE
Bit Score
The value S' is derived from the raw alignment score
S in which the statistical properties of the scoring
system used have been taken into account. Because
bit scores have been normalized with respect to the
scoring system, they can be used to compare
alignment scores from different searches.
java.lang.Double
KKAT
K_cat
turnover number
java.lang.Double
END
End of feature
Location of end of a feature
In the case of DNA, taken to be the highest base pair location from
the forward strand, regardless of sense strand for the feature.
java.lang.Integer
COVERAGE
Coverage
java.lang.Double
STRUCTURE
Protein Structure
Structure of a protein in PDBML
java.lang.String
DELTAGO
GibbsFreeEnergy
Gibbs free energy for the reaction
java.lang.Float
RANK
Taxonomy Rank
NCBI Taxonomy Rank
java.lang.String
IntronStructure
IntronStructure
java.lang.String
CitNum
Citation Number
Number of times a concept is mentioned in the literature corpus
java.lang.Integer
PMID
PMID
PubmedID
java.lang.String
GOA
GOA
When used as attribute it indicats the way the
relations was annotated
java.lang.String
URL
URL
url
java.lang.String
ubiquitous
ubiquitous
none
java.lang.Boolean
CML
CML_Chemical_Structure
Chemical Structure in Chemical Markup Language
java.lang.String
PHOPT
pH_optimum
ph optimum value
java.lang.Double
PlantType
PlantType
java.lang.String
PTM
PTM
posttranslational modification
java.lang.String
GOMATCHSCORE
GO match score
share of common go terms
java.lang.Double
Text
Text
java.lang.String
RoleClassification
Role Classification
java.lang.String
ProductType
Product Type
The type of the gene product. E.g: protein, regulator, enzyme
java.lang.String
BioProcess
BioProcess classification
java.lang.String
TFFamily
Transcription Factor Family
Transcription Factor Family
java.lang.String
TFDomain
Transcription Factor Domain
Transcription Factor Domain
java.lang.String
SF
Sigma Factor
Promoter Sigma Factor
java.lang.String
StartOfBindingSite
Start of Transcription Factor Binding Site
Start position of a transcription factor binding site in a promotor region
java.lang.String
EndOfBindingSite
End of Transcription Factor Binding Site
End position of a transcription factor binding site in a promotor region
java.lang.String
InteractionMode
Interaction Mode
Interaction Mode
java.lang.String
InteractionScore
Interaction Score
java.lang.Integer
NeighbourhoodScore
Neighbourhood Score
java.lang.Integer
FusionScore
Fusion Score
java.lang.Integer
CooccurenceScore
Cooccurence Score
java.lang.Integer
CoexpressionScore
Coexpression Score
java.lang.Integer
ExperimentalScore
Experimental Score
java.lang.Integer
DatabaseScore
Database Score
java.lang.Integer
TextminingScore
Textmining Score
java.lang.Integer
CombinedScore
Combined Score
java.lang.Integer
COGProcess
COG Process
COG Process
java.lang.String
Comment
Comment
COG Process
java.lang.String
GCContent
GC Content
Fraction of Guanine/Cytosine in nucleic acid sequence
java.lang.Float
GC3Content
GC3 Content
Fraction of Guanine/Cytosine at third base in nucleic acid coding sequence
java.lang.Float
LOC
LOC
Localisation
java.lang.String
pI
pI
Isoelectric Point
java.lang.Float
MW
MW
Molecular Weight (Daltons)
java.lang.Float
ReadingFrame
Reading Frame
Reading frames from -3 to 3
java.lang.String
Length
Length
Length
java.lang.Integer
MaxExpression
Max Expression
Max Gene Expression
java.lang.Double
MinExpression
Min Expression
Min Gene Expression
java.lang.Double
UnnormalizedMaxExpression
Unnormalized Max Expression
Unnormalized Max Gene Expression
java.lang.Double
UnnormalizedMinExpression
Unnormalized Min Expression
Unnormalized Min Gene Expression
java.lang.Double
PhylogeneticProfiling
PhylogeneticProfiling
PhylogeneticProfiling
java.lang.Boolean
Control
Control
Control experiment
java.lang.String
Target
Target
Target Experiment
java.lang.String
negativefeedback
Negative Feedback
Negative auto-regulation
java.lang.String
positivefeedback
Positive Feedback
Positive auto-regulation
java.lang.String
ffltype
FFL Type
FFL Type
java.lang.String
operongenes
Operon Genes
List of genes in the operon
java.lang.String
is_fCDS
Is fCDS
true if the gene is fCDS
java.lang.Boolean
annotatedsequence
Annotated Sequence
java.lang.String
originalannotatedsequence
Original Annotated Sequence
Original version of the annotation
java.lang.String
IMP
Inferred from Mutant Phenotype
Anything that is concluded from looking at
variations or changes, such as mutations or abnormal
levels of the product(s), of a single gene of
interest is IMP (compare IGI). Use this code for
experiments that use antibodies or other specific
inhibitors of RNA or protein activity, even though
no gene may be mutated (the rationale is that IMP is
used where an abnormal situation prevails in a cell
or organism due to the alteration of the sequence or
expression of one gene)
M
Manual curation
Manual curation
IMPEG
EC 2 GO import
EC 2 GO import
GI
By genetic evidence (mutant or transgenic study)
By genetic evidence (mutant or transgenic study)
InferredByTransformation
Inferred by transformation
IMPGE
GO 2 EC import
GO 2 EC import
UpDownAssay
Up-Down-Assay
IDA
Inferred from Direct Assay
Inferred from: Enzyme assays - In vitro
reconstitution (e.g. transcription) -
Immunofluorescence (for cellular component) - Cell
fractionation (for cellular component) - Physical
interaction/binding assay (sometimes appropriate for
cellular component or molecular function)
IMPD
Imported from database
imported from database
IEA
Inferred from Electronic Annotation
Annotations based on "hits" in sequence similarity
searches, if they have not been reviewed by curators
(curator-reviewed hits would get ISS)
IMPM
MeSH 2 CAS import
MeSH 2 CAS import
IEP
Inferred from Expression Pattern
Covers cases where the annotation is inferred from
the timing or location of expression of a gene.
Expression data will be most useful for process
annotation rather than function. For example,
several of the heat shock proteins are thought to be
involved in the process of stress response because
they are upregulated during stress conditions.
NB
Neighborhood Mapping
Neighborhood based mapping
ND
No biological Data available
Used for annotations to "unknown" molecular
function, biological process, or cellular component.
NR
Not Recorded
Used for annotations done before curators began
tracking evidence types (appears in some legacy
annotations).
IGI
Inferred from Genetic Interaction
Includes any combination of alterations in the
sequence (mutation) or expression of more than one
gene/gene product. This code can therefore cover any
of the IMP experiments that are done in a
non-wild-type background, though we prefer to use it
only when all mutations are documented.
IGC
Inferred from Genomic Context
This evidence code can be used whenever information
about the genomic context of a gene product forms
part of the evidence for a particular annotation.
Genomic context includes, but is not limited to,
such things as identity of the genes neighboring the
gene product in question (i.e. synteny), operon
structure, and phylogenetic or other whole genome
analysis.
IC
Inferred by Curator
To be used for those cases where an annotation is
not supported by any evidence, but can be reasonably
inferred by a curator from other GO annotations, for
which evidence is available.
HMMER
HMMER based mapping
HMMER based mapping
EXTERNAL2GO
EXTERNAL2GO file based mapping
external2go file based mapping
ACC
Accession based mapping
accession based mapping
IMPD_AUTOMATICALLY_CURATED
Imported from automatically curated database
imported from (automatically curated) database e.g.
UniProt/TrEMBLE
TM
Text mining based mapping
Text mining
SGD_Silenced
SGD_Silenced
IMPD_MANUALLY_CURATED
Imported from manually curated database
imported from (manually curated) database e.g.
UniProt/Swiss-Prot
INPARA
InParanoid based mapping
InParanoid based identification of ortholog groups
of proteins between pairs of species.
STOCHASTIC
Stochastic modelling
Used for concepts and relations that have been electronically
inferred using a stochastic modelling approach.
2SYN
Synonymous mapping
Synonymous mapping
SpearmansRCC
Spearman's rank correlation
Spearman's rank correlation
SGD_Verified
SGD_Verified
BLAST
BLAST based mapping
BLAST based mapping
SGD_Uncharacterized
SGD_Uncharacterized
TAS
Traceable Author Statement
Anything in a review article where the original
experiments are traceable through that article
(material from introductions to non-review papers
will sometimes meet this standard; discussion
sections should usually be regarded with greater
skepticism) - Anything found in a text book or
dictionary; usually text book material has become
common knowledge (e.g. "everybody" knows that
enolase is a glycolytic enzyme).
NAS
Non-traceable Author Statement
Database entries that don't cite a paper (e.g.
UniProt Knowledgebase records, YPD protein reports)
- Statements in papers (abstract, introduction, or
discussion) that a curator cannot trace to another
publication
RCA
Inferred from Reviewed Computational Analysis
This code is used for annotations based on a
non-sequence-based computational method, where the
results have been reviewed by an author or a
curator. As noted above, IEA should be used for any
computational annotations that are not checked for
accuracy by a curator (or by the authors of a paper
describing such analysis), and sequence comparisons
that have been reviewed use ISS. For microarray
results alone, IEP is preferred, but RCA is used
when microarray results are combined with results of
other types of large-scale experiments.
EC2GO
EC2GO file based mapping
ec2go file based mapping
FCM
Fuzzy c-means clustering
Fuzzy c-means (FCM) is a method of clustering which allows one piece of data to belong to
two or more clusters
PearsonsPMC
Pearson product-moment correlation
Pearson product-moment correlation
kmeans
Kmeans clustering based
k-means clustering
TRANS
Transitive
TRANSITIVE
GOA
By evidence from Gene Ontology annotation
By evidence from Gene Ontology annotation
ISS
Inferred from Sequence or Structural Similarity
Use this code for BLAST (or other sequence
similarity detection method) results that have been
reviewed for accuracy by a curator. If the result
has not been reviewed, use IEA. ISS can also be used
for sequence similarities reported in published
papers, if the curator thinks the result is reliable
enough. When the gene is a "homologue of," can infer
fairly detailed function and location (cellular
component) but err on the side of low resolution for
processes. For recognized domains, attribution to
any of the ontologies will probably be at low
resolution.
ISO
Inferred from Sequence Orthology
ISM
Inferred from Sequence Model
ISA
Inferred from Sequence Alignment
IPI
Inferred from Physical Interaction
Covers physical interactions between the gene
product of interest and another molecule (or ion, or
complex). For functions such as protein binding or
nucleic acid binding, a binding assay is
simultaneously IPI and IDA; IDA is preferred because
the assay directly detects the binding. We thought
that experiments detecting only antibody binding
were not suitable as evidence for function or
process (note that an effect of an antibody on an
activity or process can support a function or
process annotation, using the IMP code).
EC
Enzyme Classification
All Enzymes are ordered by Classes(e.g. 1.2.3.2)
PlantOntologyTerms
PlantOntologyTerms
Protein
Protein
A protein is comprised of one or more Polypeptides and potentially other molecules.
MolCmplx
Molecule Complex
An entity comprised of one or more molecules
NucleotideFeature
NucleotideFeature
SequenceFeature
Sequence Feature
Timepoint
Timepoint
A point in time where an observation is taken
UndefinedSemantics
UndefinedSemantics
TODO: sort out the semantics of all elements in here
SNORNAGene
snoRNA-Gene
NcRNAGene
ncRNA-Gene
XCore
XCore
TRRSubFeature
TRRSubFeature
TelomericRepeat
TelomericRepeat
TRRSubFeature
TRRSubFeature
ARS
ARS
NucleotideFeature
NucleotideFeature
PO_GrowthStage
Plant Growth and Developmental Stage (PO)
TA controlled vocabulary of growth and developmental stages
in various plants and their relationships. Examples are germination,
seedling, flowering, etc.
PlantOntologyTerms
PlantOntologyTerms
MicroArrayExperiment
MicroArrayExperiment
Microarray experiment
Experiment
Experiment
Scientific experiment
ProtDomain
Protein Domain
A Protein domain
PolypeptideFeature
PolypeptideFeature
OntologyTerms
OntologyTerms
Thing
Thing
Thing
Polypeptide
Polypeptide
A polymer of aminoacids.
InfoPolymer
InfoPolymer
A polymeric molecule that contains sequence information.
KOEN
Kegg Orthologs Enzyme
Kegg Ortholog Group of sequence similarity
KO
Kegg Ortholog Group
Kegg Ortholog Group of sequence similarity
ExpressionAffector
ExpressionAffector
UndefinedSemantics
UndefinedSemantics
TODO: sort out the semantics of all elements in here
GIDGD
Dosage Growth Defect
GenInt
Genetic Interaction
KOGE
Kegg Orthologs Gene
Kegg Ortholog Group of sequence similarity
KO
Kegg Ortholog Group
Kegg Ortholog Group of sequence similarity
Retrotransposon
Retrotransposon
NucleotideFeature
NucleotideFeature
TFBS
Transcription factor binding site
A sequence where a transcription factor binds to the DNA
NucleotideFeature
NucleotideFeature
Interaction
Interaction
Thing
Thing
Thing
Participant
Participant
A molecular biological entity that can participate in a Process or in an Interaction.
Localizable
Localizable
An abstract or physical concept that can have a location.
GenInt
Genetic Interaction
Interaction
Interaction
Protein3DStructure
Protein3DStructure
3-dimensional structure of a protein
PolypeptideFeature
PolypeptideFeature
KO
Kegg Ortholog Group
Kegg Ortholog Group of sequence similarity
Group
Group
AminoacidSequence
AminoacidSequence
Sequence
Sequence
YPrime
YPrimeElement
TRRSubFeature
TRRSubFeature
POTempStage
plant temporal stages
ontology describing Plant temporal stages (PO)
PlantOntologyTerms
PlantOntologyTerms
KOPR
Kegg Orthologs Protein
Kegg Ortholog Group of sequence similarity
KO
Kegg Ortholog Group
Kegg Ortholog Group of sequence similarity
Gene
Gene
Gene
ORF
ORF
Open reading frame
Reaction
Reaction
a chemical reaction
Process
Process
A Process
Annotation
Annotation
Thing
Thing
Thing
DNA
DNA
DNA
Polynucleotide
Polynucleotide
A polymer of nucleotides
GISGD
Synthetic Growth Defect
GenInt
Genetic Interaction
SNRNAGene
snRNA-Gene
NcRNAGene
ncRNA-Gene
sDNA
ssDNA
Single stranded deoxyribonucleic acid
DNA
DNA
DNA
Pseudogene
Pseudogene
ORF
ORF
Open reading frame
GISHI
Synthetic Haploinsufficiency
GenInt
Genetic Interaction
Z2Region
Z2Region
MatingLocusSubFeature
MatingLocusSubFeature
TF
Transcription factor
A transcription factor is a protein that regulates the expression of one or more gene by
binding to an associated DNA region (see TFBS).
Protein
Protein
A protein is comprised of one or more Polypeptides and potentially other molecules.
TO
Trait Ontology
ontology describing the different Traits which can
affect plants (TO)
OntologyTerms
OntologyTerms
TRNAGene
tRNA-Gene
NcRNAGene
ncRNA-Gene
NcRNAGene
ncRNA-Gene
NucleotideFeature
NucleotideFeature
SF
Sigma factor
A Sigma factor is a transcription factor that binds to the TATA box of a promoter,
thereby allowing the Polymerase to transcribe the downstream DNA sequence.
TF
Transcription factor
A transcription factor is a protein that regulates the expression of one or more gene
by binding to an associated DNA region (see TFBS).
PolypeptideFeature
PolypeptideFeature
SequenceFeature
Sequence Feature
FeatureContainer
FeatureContainer
These concepts serve containers for other nucleotide sequence features
NucleotideFeature
NucleotideFeature
At_Mutant
Arabidopsis Mutant
Mutant plant of Arabidopsis
Organism
Organism
Organism.
Repeat
Repeat
NucleotideFeature
NucleotideFeature
Organism
Organism
Organism.
Taxon
Taxon
Any Taxonomic Entity such as species families etc
NASEQ
Nucleic Acid Sequence
Nucleic Acid Sequence
Sequence
Sequence
Publication
Publication
none
UndefinedSemantics
UndefinedSemantics
TODO: sort out the semantics of all elements in here
QTL
Quantitative Trait Locus
Quantitative Trait Locus
NucleotideFeature
NucleotideFeature
Transporter
Transporter
A protein that transports compounds through membranes between different cellular
compartments.
Protein
Protein
A protein is comprised of one or more Polypeptides and potentially other molecules.
CDEII
CDEII
CentromereSubFeature
CentromereSubFeature
TRR
TelomericRegion
NucleotideFeature
NucleotideFeature
TARGETSEQ
Probe Set Target Sequence
The relatively small less than 600 nucleotide
sequence segment from the 3' end of the consensus or
the exemplar sequence; used to design the probes for
any given probe set.
NASEQ
Nucleic Acid Sequence
Nucleic Acid Sequence
RRNAGene
rRNA-Gene
NcRNAGene
ncRNA-Gene
Protcmplx
Protein complex
Protein Complex consists of several subunits
Protein
Protein
A protein is comprised of one or more Polypeptides and potentially other molecules.
Comp
Compound
a chemical compound
Molecule
Molecule
A molecule is comprised of one or more atoms that form a single component through
covalent bonds.
ECorg
ECorg
Used by Brenda, a number belongs to one EC and one
Organism
EC
Enzyme Classification
All Enzymes are ordered by Classes(e.g. 1.2.3.2)
ORF
ORF
Open reading frame
NucleotideFeature
NucleotideFeature
NonTranscribedRegion
NonTranscribedRegion
NucleotideFeature
NucleotideFeature
Cultivar
Plant Cultivar
Variation of a plant species arising in cultivation
and propagated for some unusual characteristic, such
as leaf colour or shape.
Organism
Organism
Organism.
AHDPO
Phenotype Ontology
Arabidopsis Hormone Database, Phenotype Ontology
http://nar.oxfordjournals.org/cgi/content/full/37/suppl_1/D975?ck=nck
OntologyTerms
OntologyTerms
SignallingPathway
SignallingPathway
processes of signal transduction involve ordered sequences of biochemical reactions inside
the cell, which are carried out by enzymes and activated by second messengers, resulting in a signal
transduction pathway.
Path
Pathway
Biological Pathway
Path
Pathway
Biological Pathway
ProcessSequence
ProcessSequence
GISR
Synthetic Rescue
GenInt
Genetic Interaction
PO_PlantStructure
Plant Structure (PO)
The controlled vocabulary of plant structures representing organs,
tissue and cell types. Examples are stamen, gynoecium, petal, parenchyma,
guard cell, etc
PlantOntologyTerms
PlantOntologyTerms
CDEI
CDEI
CentromereSubFeature
CentromereSubFeature
SubtelomereSubFeature
SubtelomereSubFeature
NucleotideFeature
NucleotideFeature
CDEIII
CDEIII
CentromereSubFeature
CentromereSubFeature
MultiGeneLocus
MultiGeneLocus
NucleotideFeature
NucleotideFeature
RNA
RNA
Ribonucleic Acid. A polymer of riboses with pyrimidine and purine bases.
Polynucleotide
Polynucleotide
A polymer of nucleotides
Transport
Transport
Process
Process
A Process
GISL
Synthetic Lethality
GenInt
Genetic Interaction
BioProc
Biological_Process
Biological_Process (GO)
GeneOntologyTerms
GeneOntologyTerms
RRNA
rRNA
ncRNA
ncRNA
GIPE
Phenotypic Enhancemant
GenInt
Genetic Interaction
MolCmplx
Molecule Complex
An entity comprised of one or more molecules
Participant
Participant
A molecular biological entity that can participate in a Process or in an Interaction.
Sequence
Sequence
Thing
Thing
Thing
Space
Space
Localizable
Localizable
An abstract or physical concept that can have a location.
STR
XElementCombinatorialRepeat
SubtelomereSubFeature
SubtelomereSubFeature
GIPS
Phenotypic Suppression
GenInt
Genetic Interaction
Taxon
Taxon
Any Taxonomic Entity such as species families etc
Thing
Thing
Thing
MetabolicPathway
MetabolicPathway
series of chemical reactions occurring within a cell.
Path
Pathway
Biological Pathway
Tissue
Tissue
Part of an organism consisting of an aggregate of cells having a similar structure and
function
Space
Space
UndefinedSemantics
UndefinedSemantics
TODO: sort out the semantics of all elements in here
Thing
Thing
Thing
SIRNA
siRNA
Small Interfering RNA
ncRNA
ncRNA
Plant_Hormone
Plant Hormone
Plant Hormone treatment
Treatment
Treatment
Any biotic or abiotic treatment like pathogens,
wound or drought to any host
MeSH
Medical Subject Headings
NLM's controlled vocabulary, used to characterize
the content of MEDLINE citations
OntologyTerms
OntologyTerms
CelComp
Cellular_Component
Cellular Component (GO)
GeneOntologyTerms
GeneOntologyTerms
Environment
Environment
Treatment or surrounding conditions
Space
Space
InfoPolymer
InfoPolymer
A polymeric molecule that contains sequence information.
Molecule
Molecule
A molecule is comprised of one or more atoms that form a single component through
covalent bonds.
ARSCons
ARS-Consensus
NucleotideFeature
NucleotideFeature
CHEM
Chemical
Ontology of chemicals
OntologyTerms
OntologyTerms
SequenceFeature
Sequence Feature
Thing
Thing
Thing
XRegion
XRegion
MatingLocusSubFeature
MatingLocusSubFeature
Metabolite
Metabolite
Metabolite
Comp
Compound
a chemical compound
Drug
Drug
a medical drug
Comp
Compound
a chemical compound
Process
Process
A Process
Localizable
Localizable
An abstract or physical concept that can have a location.
Thing
Thing
Thing
TRRSubFeature
TRRSubFeature
NucleotideFeature
NucleotideFeature
PhysInt
Physical Interaction
Interaction
Interaction
HierarchyNode
Hierarchy Node
a node in a graph hierarchy dendrogram
UndefinedSemantics
UndefinedSemantics
TODO: sort out the semantics of all elements in here
GeneCassette
GeneCassette
NucleotideFeature
NucleotideFeature
CentromereSubFeature
CentromereSubFeature
NucleotideFeature
NucleotideFeature
Localizable
Localizable
An abstract or physical concept that can have a location.
Thing
Thing
Thing
Chromosome
Chromosome
Chromosome
FeatureContainer
FeatureContainer
These concepts serve containers for other nucleotide sequence features
GIDR
Dosage Rescue
GenInt
Genetic Interaction
GIDL
Dosage Lethality
GenInt
Genetic Interaction
STBS
SubtelomericBindingSite
SubtelomereSubFeature
SubtelomereSubFeature
PWM
Position specific Weight Matrix
pwm represents a scoring scheme for potential dna binding sites of a
transcription factor
UndefinedSemantics
UndefinedSemantics
TODO: sort out the semantics of all elements in here
Molecule
Molecule
A molecule is comprised of one or more atoms that form a single component through covalent
bonds.
Participant
Participant
A molecular biological entity that can participate in a Process or in an Interaction.
Centromere
Centromere
NucleotideFeature
NucleotideFeature
GeneOntologyTerms
GeneOntologyTerms
OntologyTerms
OntologyTerms
Z1Region
Z1Region
MatingLocusSubFeature
MatingLocusSubFeature
PlantOntologyTerms
PlantOntologyTerms
OntologyTerms
OntologyTerms
Scaffold
Scaffold
A sequence region which has no physical mapping to one of the main linkage groups
(Chromosomes)
FeatureContainer
FeatureContainer
These concepts serve containers for other nucleotide sequence features
SNORNA
snoRNA
ncRNA
ncRNA
ProcessSequence
ProcessSequence
Thing
Thing
Thing
Treatment
Treatment
Any biotic or abiotic treatment like pathogens,
wound or drought to any host
Thing
Thing
Thing
MolFunc
Molecular_Function
Molecular Function (GO)
GeneOntologyTerms
GeneOntologyTerms
MatingLocus
MatingLocus
NucleotideFeature
NucleotideFeature
Enzyme
Enzyme
An Enzyme is a Protein that catalyzes a chemical reaction.
Protein
Protein
A protein is comprised of one or more Polypeptides and potentially other molecules.
PublicationList
PublicationList
List of publications
UndefinedSemantics
UndefinedSemantics
TODO: sort out the semantics of all elements in here
TRNA
tRNA
Transfer RNA
ncRNA
ncRNA
YRegion
YRegion
MatingLocusSubFeature
MatingLocusSubFeature
Group
Group
Thing
Thing
Thing
ProtFam
Protein Family
Proteins which share a common family
Annotation
Annotation
WRegion
WRegion
MatingLocusSubFeature
MatingLocusSubFeature
Polynucleotide
Polynucleotide
A polymer of nucleotides
InfoPolymer
InfoPolymer
A polymeric molecule that contains sequence information.
ncRNA
ncRNA
RNA
RNA
Ribonucleic Acid. A polymer of riboses with pyrimidine and purine bases.
Operon
Operon
An operon is comprised of a promoter, an operator, one or more genes and a terminator.
NucleotideFeature
NucleotideFeature
StrucProt
Structural Protein
A protein that serves structural purposes.
Protein
Protein
A protein is comprised of one or more Polypeptides and potentially other molecules.
MatingLocusSubFeature
MatingLocusSubFeature
NucleotideFeature
NucleotideFeature
GRO
Cereal Plant Growth Stages
The controlled vocabulary of growth and
developmental stages in various cereal plants.
Examples are germination, seedling, booting,
flowering, etc. Available only for rice, maize,
sorghum, wheat, wheat, oat and barley
PlantOntologyTerms
PlantOntologyTerms
EST
EST
"single-pass" cDNA sequence, or Expressed Sequence
Tag
NASEQ
Nucleic Acid Sequence
Nucleic Acid Sequence
Experiment
Experiment
Scientific experiment
UndefinedSemantics
UndefinedSemantics
TODO: sort out the semantics of all elements in here
dDNA
dsDNA
Double stranded deoxyribonucleic acid
DNA
DNA
DNA
Disease
Disease
Human Diseases
ExpressionAffector
ExpressionAffector
MRNA
mRNA
Messenger RNA
RNA
RNA
Ribonucleic Acid. A polymer of riboses with pyrimidine and purine bases.
LTR
Long_terminal_repeat
TRRSubFeature
TRRSubFeature
SNRNA
snRNA
ncRNA
ncRNA
MeshDescriptor
MeSH Descriptor
A descriptor record from MeSH
Thing
Thing
Thing
MeshQualifier
MeSH Qualifier
A qualifier from MeSH
Thing
Thing
Thing
MeshConcept
MeSH Concept
A concept from MeSH
Thing
Thing
Thing
MeshSemanticType
MeSH Semantic Type
A semantic type from MeSH
Thing
Thing
Thing
MeshPharmacologicalAction
MeSH Pharmacological Action
A parmacological action from MeSH
Thing
Thing
Thing
MeshSubstance
MeSH Substance
A substance from MeSH
Thing
Thing
Thing
Operator
Operator
Operator
NucleotideFeature
NucleotideFeature
Terminator
Terminator
Terminator
NucleotideFeature
NucleotideFeature
COG
COG Class
COG Class
Annotation
Annotation
COGCategory
COG Class Category
COG Class Category
Annotation
Annotation
Promoter
Promoter
Promoter
NucleotideFeature
NucleotideFeature
FFL
Feed Forward Loop
Feed Forward Loop
Thing
Thing
Thing
Shim
Spacer sequence
NucleotideFeature
NucleotideFeature
RBS
Ribosome Binding Site
NucleotideFeature
NucleotideFeature
CDS
Coding sequence
Coding sequence
ORF
ORF
Open reading frame
co_by
cofactored_by
none
false
false
false
false
has_participant
has_participant
P has_participant C if and only if: given any
process p that instantiates P there is some
continuant c, and some time t, such that: c
instantiates C at t and c participates in p at t
participates_in
true
false
false
false
undefined_semantics
undefined_semantics
none
false
false
false
false
r
is_related_to
Root relation type
is_related_to
false
true
true
false
gi_sgd
inflicts_growth_defect_on
growth_defect_inflicted_by
true
false
false
false
gi
interacts_genetically_with
Gene->Gene
interacts_genetically_with
false
false
false
false
is_a
is_a
(Meta) is_a
This relation type represents when two classes are represented as Ondex Concepts, that there is a
class level is-a relationship between the two classes.
is_a
false
true
false
true
physical
has_physical_relation_with
none
false
false
false
false
rp_by
replaced_by
replaces
false
false
false
false
physical
has_physical_relation_with
none
false
false
false
false
gi_shi
inflicts_haploinsufficiency_on
haploinsufficiency_inflicted_by
true
false
false
false
gi
interacts_genetically_with
Gene->Gene
interacts_genetically_with
false
false
false
false
has_nuclFeature
has_nucleotide_feature
NucleotideSequence->NucleotideFeature
is_nucleotide_feature_of
true
false
false
true
has_feature
has_feature
Sequence->SequenceFeature
is_feature_of
true
false
false
true
ca_by
catalyzed_by
catalyzation of a reaction by a catalyst
catalyzes
true
false
false
false
has_agent
has_agent
As for has_participant, but with the additional
condition that the component instance is causally
active in the relevant process
is_agent_of
true
false
false
false
taken_by
taken_by
takes
true
false
false
false
part_pass
participates_passively_in
has_passive_participant
true
false
false
false
in_by
inhibited_by
inhibition of a gene's expression by a transcription factor
inhibits
true
false
false
false
rg_by
regulated_by
TF->Gene
regulates
true
false
false
false
r
is_related_to
Root relation type
is_related_to
false
true
true
false
ex_by
expressed_by
interactions via DNA binding
none
false
false
false
false
rg_by
regulated_by
TF->Gene
regulates
true
false
false
false
occ_in
occurs_in
has_occurrence_of
false
false
false
false
r
is_related_to
Root relation type
is_related_to
false
true
true
false
cooc_wi
cooccurs_with
none
false
false
false
false
r
is_related_to
Root relation type
is_related_to
false
true
true
false
asso_wi
associated_with
none
false
false
false
false
r
is_related_to
Root relation type
is_related_to
false
true
true
false
physical
has_physical_relation_with
none
false
false
false
false
r
is_related_to
Root relation type
is_related_to
false
true
true
false
textual_relationship
textual_relationship
none
false
false
false
false
physical
has_physical_relation_with
none
false
false
false
false
catalyzes
catalyzes
Enzyme->Reaction
is_catalyzed_by
true
false
false
false
modifies
modifies
Participant->Process
is_modified_by
true
false
false
false
phosphorylated_by
phosphorylated_by
Protein->Protein
phosphorylates
false
false
false
false
ptm_by
post-translationally_modified_by
post-translationally_modifies
false
false
false
false
not_located_in
is_not_located_in
is_not_location_of
true
false
false
false
not_annotated_by
not_annotated_with
does_not_annotate
true
false
false
false
en_by
is_encoded_by
Polypeptide->Gene
encodes
true
false
false
false
info_transd
information_transduction
none
false
false
false
false
pub_in
published_in
Thing->Publication
publication_features
false
false
false
false
phys_intbio
physical_IB_relation
physical_IB_relation
false
false
true
false
direct_correlation_with
direct_correlation_with
Entities that are directly correlated (+ve coefficiant)
none
false
false
false
false
correlated_with
correlated_with
none
false
false
false
false
gi_ps
suppresses_phenotype_of
phenotype_suppressed_by
true
false
false
false
gi
interacts_genetically_with
Gene->Gene
interacts_genetically_with
false
false
false
false
has_chem_f_p
has_chemical_functional_parent
Used to denote the relationship between two
molecular entities (or classes of entities), one of
which possesses one or more chacteristic groups from
which the other can be derived by functional
modification. This relationship is especially useful
to demonstrate the relationships between a number of
functionalised entities and a common
less-functionalised parent.
is_chemical_functional_parent_of
true
false
false
false
chem_rel
chemical_relationship
none
false
false
false
false
correlated_with
correlated_with
none
false
false
false
false
math
mathematical_relationship
superclass for mathematical relations
none
false
false
false
false
demethylated_by
demethylated_by
demethylates
false
false
false
false
ptm_by
post-translationally_modified_by
post-translationally_modifies
false
false
false
false
performs_transport
performs_transport
Transporter->Transport
transport_performed_by
true
false
false
false
modifies
modifies
Participant->Process
is_modified_by
true
false
false
false
gi_sr
rescues
rescued_by
true
false
false
false
gi
interacts_genetically_with
Gene->Gene
interacts_genetically_with
false
false
false
false
gi_sl
causes_lethality_with
lethality_caused_with_by
true
false
false
false
gi
interacts_genetically_with
Gene->Gene
interacts_genetically_with
false
false
false
false
homologue
homologue
gene is homologue to other gene
none
false
false
false
false
h_s_s
has_similar_sequence
blastbased homolog proteins of different species
has_similar_sequence
false
false
false
false
proper_part_of
proper_part_of
As for part_of, with the additional constraint that
subject and object are distinct
has_proper_part
false
false
false
false
part_of
part_of
For continuants: C part_of C' if and only if: given
any c that instantiates C at a time t, there is some
c' such that c' instantiates C' at time t, and c
*part_of* c' at t. For processes: P part_of P' if
and only if: given any p that instantiates P at a
time t, there is some p' such that p' instantiates
P' at time t, and p *part_of* p' at t. (Here
*part_of* is the instance-level part-relation.)
has_part
true
true
false
true
hormone_treated
hormone treatment (treated case)
hormone_treated relates an experiment with a hormone.
experiment -> hormone_treated -> hormone should be interpreted as:
This experiment involves the application of hormone.
none
false
false
false
false
with_treatment
involves hormone
none
false
false
false
false
has_observ_pheno
has_observed_phenotype
Result of a experiment produces a phenotype
none
false
false
false
false
has_attributive_relation_with
has_attributive_relation_with
none
false
false
false
false
phys_intbio
physical_IB_relation
physical_IB_relation
false
false
true
false
physical
has_physical_relation_with
none
false
false
false
false
KI
KI
none
false
false
false
false
undefined_semantics
undefined_semantics
none
false
false
false
false
glycosylated_by
glycosylated_by
glycosylates
false
false
false
false
ptm_by
post-translationally_modified_by
post-translationally_modifies
false
false
false
false
gi_pe
enhances_phenotype_of
phenotype_enhanced_by
true
false
false
false
gi
interacts_genetically_with
Gene->Gene
interacts_genetically_with
false
false
false
false
h_chem_p_hybride
has_chemical_parent_hybride
Used to denote the relationship between an entity
and its parent hydride (defined by IUPAC as "an
unbranched acyclic or cyclic structure or an
acyclic/cyclic structure having a semisystematic or
trivial name to which only hydrogen atoms are
attached").
is_chemical_parent_hybride
true
false
false
false
chem_rel
chemical_relationship
none
false
false
false
false
do_by
effluxes_from
is_efflux_from
true
false
false
false
given_by
given_by
gives
true
false
false
false
situated_to
situated_to
A transcription factor binding site is situated next to a Gene.
situated_to
false
false
true
true
physical
has_physical_relation_with
none
false
false
false
false
part_of
part_of
For continuants: C part_of C' if and only if: given
any c that instantiates C at a time t, there is some
c' such that c' instantiates C' at time t, and c
*part_of* c' at t. For processes: P part_of P' if
and only if: given any p that instantiates P at a
time t, there is some p' such that p' instantiates
P' at time t, and p *part_of* p' at t. (Here
*part_of* is the instance-level part-relation.)
has_part
true
true
false
true
physical
has_physical_relation_with
none
false
false
false
false
is_annotated_by
is_annotated_by
Thing->Annotation
annotates
false
false
false
false
has_attributive_relation_with
has_attributive_relation_with
none
false
false
false
false
upstream
is_upstream_of
is_downstream_from
false
false
false
true
5pNeighbour
is_5'_neighbour_of
is_3'_neighbour_of
true
false
false
false
math
mathematical_relationship
superclass for mathematical relations
none
false
false
false
false
physical
has_physical_relation_with
none
false
false
false
false
methylated_by
methylated_by
methylates
false
false
false
false
ptm_by
post-translationally_modified_by
post-translationally_modifies
false
false
false
false
is_tautomer_of
is_tautomer_of
A cyclic relationship used to show the
interrelationship between two tautomers, where the
differences between the structures are significant
enough to warrant their separate inclusion in ChEBI.
none
false
false
false
false
chem_rel
chemical_relationship
none
false
false
false
false
gi_dl
dosage_lethality
dosage_lethality
true
false
false
false
gi
interacts_genetically_with
Gene->Gene
interacts_genetically_with
false
false
false
false
gi_dr
dosage_rescue
dosage_rescue
true
false
false
false
gi
interacts_genetically_with
Gene->Gene
interacts_genetically_with
false
false
false
false
modifies
modifies
Participant->Process
is_modified_by
true
false
false
false
part_act
participates_actively_in
has_active_participant
true
false
false
false
transcribes_to
transcribes_to
Gene->mRNA
is_transcribed_from
true
false
false
false
info_transd
information_transduction
none
false
false
false
false
info_transd
information_transduction
none
false
false
false
false
phys_intbio
physical_IB_relation
physical_IB_relation
false
false
true
false
equ
is_equivalent_to
is_equivalent_to
false
true
true
true
physical
has_physical_relation_with
none
false
false
false
false
part_pass
participates_passively_in
has_passive_participant
true
false
false
false
participates_in
participates_in
Participant->Process
has_participant
true
false
false
false
err
Error
none
false
false
false
false
undefined_semantics
undefined_semantics
none
false
false
false
false
given_by
given_by
gives
true
false
false
false
part_pass
participates_passively_in
has_passive_participant
true
false
false
false
is_part_of
is_part_of
Molecule->MoleculeCmplx
has_part
true
false
false
true
part_of
part_of
For continuants: C part_of C' if and only if: given
any c that instantiates C at a time t, there is some
c' such that c' instantiates C' at time t, and c
*part_of* c' at t. For processes: P part_of P' if
and only if: given any p that instantiates P at a
time t, there is some p' such that p' instantiates
P' at time t, and p *part_of* p' at t. (Here
*part_of* is the instance-level part-relation.)
has_part
true
true
false
true
st_fr
state_change_from
entry2 has a state change from entry1
state_change_to
true
false
false
false
physical
has_physical_relation_with
none
false
false
false
false
is_chem_sub_gr_from
is_chemical_substituent_group_from
Indicates the relationship between a substituent
group (or atom) and its parent molecular entity,
from which it is formed by loss of one or more
protons or simple groups.
has_chemical_substituent_group
true
false
false
false
chem_rel
chemical_relationship
none
false
false
false
false
has_domain
has_protein_domain
AminoacidSequence->ProteinDomain
is_protein_domain_of
true
false
false
true
has_feature
has_feature
Sequence->SequenceFeature
is_feature_of
true
false
false
true
contrib
contributes_to
has_contributor
false
false
false
false
physical
has_physical_relation_with
none
false
false
false
false
ac_by
activated_by
activation of a gene's expression by a transcription factor
activates
true
false
false
false
rg_by
regulated_by
TF->Gene
regulates
true
false
false
false
subfeature_of
is_subfeature_of
has_subfeature
false
false
false
false
rel_seq_pos
has_relative_sequence_position
has_relative_sequence_position
false
true
true
true
5pNeighbour
is_5'_neighbour_of
is_3'_neighbour_of
true
false
false
false
rel_seq_pos
has_relative_sequence_position
has_relative_sequence_position
false
true
true
true
transformation_of
transformation_of
Relation between two classes, in which instances
retain their identity yet change their
classification by virtue of some kind of
transformation. Formally: C transformation_of C' if
and only if given any c and any t, if c instantiates
C at time t, then for some t', c instantiates C' at
t' and t' earlier t, and there is no t2 such that c
instantiates C at t2 and c instantiates C' at t2.
none
false
false
false
false
physical
has_physical_relation_with
none
false
false
false
false
phys_int
interacts_physically_with
Participant->Participant
interacts_physically_with
false
false
false
false
it_wi
interacts_with
Thing->Thing
interacts_with
false
false
true
false
has_relative_position
has_relative_position
has_relative_position
false
true
true
true
physical
has_physical_relation_with
none
false
false
false
false
is_conjugate
is_conjugate
Cyclic relationships which are used mainly between
acids and their conjugate bases.
is_conjugate
false
false
true
false
chem_rel
chemical_relationship
none
false
false
false
false
has_sequence
has_sequence
InfoPolymer->Sequence
is_sequence_of
true
false
false
false
has_attributive_relation_with
has_attributive_relation_with
none
false
false
false
false
translates_to
translates_to
mRNA->Polypeptide
is_translated_from
true
false
false
false
info_transd
information_transduction
none
false
false
false
false
gi
interacts_genetically_with
Gene->Gene
interacts_genetically_with
false
false
false
false
it_wi
interacts_with
Thing->Thing
interacts_with
false
false
true
false
cs_by
consumed_by
consumes
true
false
false
false
taken_by
taken_by
takes
true
false
false
false
acetylated_by
acetylated_by
acetylates
false
false
false
false
ptm_by
post-translationally_modified_by
post-translationally_modifies
false
false
false
false
not_annotated_by
not_annotated_with
does_not_annotate
true
false
false
false
has_attributive_relation_with
has_attributive_relation_with
none
false
false
false
false
elongates
elongates
Catalysis of chain elongation
is_elongated_by
true
false
false
false
phys_intbio
physical_IB_relation
physical_IB_relation
false
false
true
false
chem_rel
chemical_relationship
none
false
false
false
false
physical
has_physical_relation_with
none
false
false
false
false
sim
sim
none
false
false
false
false
undefined_semantics
undefined_semantics
none
false
false
false
false
enz_int
enz_int
Two compounds have an unspecified enzymatic
interaction
none
false
false
false
false
phys_int
interacts_physically_with
Participant->Participant
interacts_physically_with
false
false
false
false
has_participant
has_participant
P has_participant C if and only if: given any
process p that instantiates P there is some
continuant c, and some time t, such that: c
instantiates C at t and c participates in p at t
participates_in
true
false
false
false
undefined_semantics
undefined_semantics
none
false
false
false
false
assoc_hormone
is associated with hormone
This would typically relate a gene or an experiment with a hormone.
Interpretation should be:
This gene or experiment involved this hormone (but more explicit information of how is not known).
none
false
false
false
false
with_treatment
involves hormone
none
false
false
false
false
has_attributive_relation_with
has_attributive_relation_with
none
false
false
false
false
r
is_related_to
Root relation type
is_related_to
false
true
true
false
located_in
located_in
Localizable->Space
is_location_of
true
false
false
true
has_relative_position
has_relative_position
has_relative_position
false
true
true
true
participates_not
participates_not
has_not_participant
true
false
false
false
not_annotated_by
not_annotated_with
does_not_annotate
true
false
false
false
coloc
colocalized_with
colocalized_with
false
true
true
true
has_relative_position
has_relative_position
has_relative_position
false
true
true
true
with_treatment
involves hormone
none
false
false
false
false
r
is_related_to
Root relation type
is_related_to
false
true
true
false
member_of
member_of
Used for characterisation of grouping relationships, e.g. a reaction is member of a
pathway.
has_member
true
true
false
true
has_attributive_relation_with
has_attributive_relation_with
none
false
false
false
false
hormone_control
hormone treatment (control case)
hormone_control relates an experiment with a hormone.
experiment -> hormone_control -> hormone should be interpreted as:
This experiment has no hormone treatment applied.
none
false
false
false
false
with_treatment
involves hormone
none
false
false
false
false
hs_ch
has_chemical
has Ec or CAS ID
is_chemical_in
true
false
false
false
phys_intbio
physical_IB_relation
physical_IB_relation
false
false
true
false
has_mutated_gene
has_mutated_gene
has_mutated_gene relates an organism/cultivar/mutant with a reference/canonical gene
Interpretation:
Organism has a mutant version of some reference/canonical gene, where the reference gene would be
regarded one from a public database.
is_mutated_gene_in
false
false
false
false
phys_intbio
physical_IB_relation
physical_IB_relation
false
false
true
false
pd_by
produced_by
produces
true
false
false
false
given_by
given_by
gives
true
false
false
false
instance_of
instance_of
A relation between an instance and a class. For
components: a primitive relation between a component
instance and a class which it instantiates at a
specific time. For processes: a primitive relation,
between a process instance and a class which it
instantiates, holding independently of time
has_instance
true
false
false
false
physical
has_physical_relation_with
none
false
false
false
false
ipara
inparalogue
gene is inparalogue of another gene
inparalogue
false
false
false
false
para
paralogue
gene is paralogue to other gene
none
false
false
true
false
di_fr
dissociated_from
none
false
false
false
false
undefined_semantics
undefined_semantics
none
false
false
false
false
has_function
has_function
is_function_of
true
false
false
false
has_attributive_relation_with
has_attributive_relation_with
none
false
false
false
false
rg_by
regulated_by
TF->Gene
regulates
true
false
false
false
phys_intbio
physical_IB_relation
physical_IB_relation
false
false
true
false
ubiquinated_by
ubiquinated_by
none
false
false
false
false
ptm_by
post-translationally_modified_by
post-translationally_modifies
false
false
false
false
gi_dgd
dosage_growth_defect
dosage_growth_defect
true
false
false
false
gi
interacts_genetically_with
Gene->Gene
interacts_genetically_with
false
false
false
false
ptm_by
post-translationally_modified_by
post-translationally_modifies
false
false
false
false
phys_intbio
physical_IB_relation
physical_IB_relation
false
false
true
false
5pOverlap
overlaps_5'_of
overlaps_3'_of
true
false
false
false
5pNeighbour
is_5'_neighbour_of
is_3'_neighbour_of
true
false
false
false
id_by
indirect_effect
indirect effect without molecular details (same as used for GErel)
none
false
false
false
false
physical
has_physical_relation_with
none
false
false
false
false
derives_from
derives_from
Derivation on the instance level (*derives_from*) holds between distinct material
continuants when one succeeds the other across a temporal divide in such
a way that at least a biologically significant
portion of the matter of the earlier continuant is
inherited by the later. We say that one class C
derives_from class C' if instances of C are
connected to instances of C' via some chain of
instance-level derivation relations. Example:
osteocyte derives_from osteoblast. Formally: C
derives_immediately_from C' if and only if: given
any c and any t, if c instantiates C at time t, then
there is some c' and some t', such that c'
instantiates C' at t' and t' earlier-than t and c
*derives_from* c'. C derives_from C' if and only if:
there is an chain of immediate derivation relations
connecting C to C'.
derivable_to
true
false
false
false
physical
has_physical_relation_with
none
false
false
false
false
it_wi
interacts_with
Thing->Thing
it_mi
false
false
true
false
phys_intbio
physical_IB_relation
physical_IB_relation
false
false
true
false
it_mi
missing_interaction
Thing->Thing
it_wi
false
false
true
false
has_feature
has_feature
Sequence->SequenceFeature
is_feature_of
true
false
false
true
has_attributive_relation_with
has_attributive_relation_with
none
false
false
false
false
anto
anto
none
false
false
false
false
undefined_semantics
undefined_semantics
none
false
false
false
false
is_enantiomer_of
is_enantiomer_of
A cyclic relationship used when two entities are
enantiomers of each other. An entity may have this
relationship with only one other entity.
none
false
false
false
false
chem_rel
chemical_relationship
none
false
false
false
false
cat_c
part_of_catalyzing_class
none
false
false
false
false
part_of
part_of
For continuants: C part_of C' if and only if: given
any c that instantiates C at a time t, there is some
c' such that c' instantiates C' at time t, and c
*part_of* c' at t. For processes: P part_of P' if
and only if: given any p that instantiates P at a
time t, there is some p' such that p' instantiates
P' at time t, and p *part_of* p' at t. (Here
*part_of* is the instance-level part-relation.)
has_part
true
true
false
true
preceded_by
preceded_by
Used for keggenzymecentric
on P preceded_by P' if and only if: given any
process p that instantiates P at a time t, there is
some process p' such that p' instantiates P' at time
t', and t' is earlier than t.
precedes
true
false
false
true
physical
has_physical_relation_with
none
false
false
false
false
adjacent_to
adjacent_to
n C adjacent to C' if and only if: given any
instance c that instantiates C at a time t, there is
some c' such that: c' instantiates C' at time t and
c and c' are in spatial proximity
adjacent_to
false
false
false
false
has_relative_position
has_relative_position
has_relative_position
false
true
true
true
unkwn
unkwn
none
false
false
false
false
undefined_semantics
undefined_semantics
none
false
false
false
false
is_hyperym_of
is_hypernym_of
none
false
false
false
false
textual_relationship
textual_relationship
none
false
false
false
false
participates_in
participates_in
Participant->Process
has_participant
true
false
false
false
phys_intbio
physical_IB_relation
physical_IB_relation
false
false
true
false
para
paralogue
gene is paralogue to other gene
none
false
false
true
false
homologue
homologue
gene is homologue to other gene
none
false
false
false
false
dephosphorylated_by
dephosphorylated_by
dephosphorylates
false
false
false
false
ptm_by
post-translationally_modified_by
post-translationally_modifies
false
false
false
false
rel_seq_pos
has_relative_sequence_position
has_relative_sequence_position
false
true
true
true
phys_intbio
physical_IB_relation
physical_IB_relation
false
false
true
false
re_by
repressed_by
gene's expression is repressed by transcripiton factor
none
false
false
false
false
rg_by
regulated_by
TF->Gene
regulates
true
false
false
false
inv_in
is_involved_in
Involvement in something e.g. disease
involves
true
false
false
false
phys_intbio
physical_IB_relation
physical_IB_relation
false
false
true
false
5pAdjacent
is_5'_adjacent_to
is_3'_adjacent_to
true
false
false
false
upstream
is_upstream_of
is_downstream_from
false
false
false
true
inverse_correlation_with
inverse_correlation_with
Entities that are inversely correlated (-ve coefficiant)
none
false
false
false
false
correlated_with
correlated_with
none
false
false
false
false
part_act
participates_actively_in
has_active_participant
true
false
false
false
participates_in
participates_in
Participant->Process
has_participant
true
false
false
false
im_of
intermediate_of
has_intermediate
true
false
false
false
chem_rel
chemical_relationship
none
false
false
false
false
pr_by
preceded_by
A is the direct outcome of B
precedes
true
false
false
true
preceded_by
preceded_by
Used for keggenzymecentric
on P preceded_by P' if and only if: given any
process p that instantiates P at a time t, there is
some process p' such that p' instantiates P' at time
t', and t' is earlier than t.
precedes
true
false
false
true
der
der
none
false
false
false
false
undefined_semantics
undefined_semantics
none
false
false
false
false
dev
dev
none
false
false
false
false
undefined_semantics
undefined_semantics
none
false
false
false
false
pu_by
taken_up_by
takes_up
true
false
false
false
taken_by
taken_by
takes
true
false
false
false
hormone_treatment
involves hormone
none
false
false
false
false
undefined_semantics
undefined_semantics
none
false
false
false
false
s_isp
s_isp
none
false
false
false
false
undefined_semantics
undefined_semantics
none
false
false
false
false
integral_part_of
integral_part_of
C integral_part_of C' if and only if: C part_of C'
AND C' has_part C
has_integral_part
false
false
false
false
part_of
part_of
For continuants: C part_of C' if and only if: given
any c that instantiates C at a time t, there is some
c' such that c' instantiates C' at time t, and c
*part_of* c' at t. For processes: P part_of P' if
and only if: given any p that instantiates P at a
time t, there is some p' such that p' instantiates
P' at time t, and p *part_of* p' at t. (Here
*part_of* is the instance-level part-relation.)
has_part
true
true
false
true
h_s_s
has_similar_sequence
blastbased homolog proteins of different species
has_similar_sequence
false
false
false
false
phys_intbio
physical_IB_relation
physical_IB_relation
false
false
true
false
sensu
sensu
GO concept names contain a sensu part which we break
up into seperate concepts and relations
inverse_sensu
false
false
false
false
phys_intbio
physical_IB_relation
physical_IB_relation
false
false
true
false
h_pwm
has_pwm
transcription factor binding site (TFBS) has position-specific weight matrix (PWM)
is_pwm_of
false
false
false
false
has_attributive_relation_with
has_attributive_relation_with
none
false
false
false
false
has_agent
has_agent
As for has_participant, but with the additional
condition that the component instance is causally
active in the relevant process
is_agent_of
true
false
false
false
has_participant
has_participant
P has_participant C if and only if: given any
process p that instantiates P there is some
continuant c, and some time t, such that: c
instantiates C at t and c participates in p at t
participates_in
true
false
false
false
not_function
has_not_function
is_not_function_of
true
false
false
false
not_annotated_by
not_annotated_with
does_not_annotate
true
false
false
false
sh_im
share_intermediate
shared with two successive reactions (ECrel) or intermediate of two interacting proteins
(PPrel)
none
false
false
false
false
has_relative_position
has_relative_position
has_relative_position
false
true
true
true
ortho
orthologue
blastbased ortholog proteins of different species
orthologue
false
false
true
false
homologue
homologue
gene is homologue to other gene
none
false
false
false
false
bi_to
binds_to
Molecule->Molecule
bound_by
false
false
false
false
phys_int
interacts_physically_with
Participant->Participant
interacts_physically_with
false
false
false
false
att
att
none
false
false
false
false
undefined_semantics
undefined_semantics
none
false
false
false
false
qualifiedBy
qualifiedBy
A MeSH description is qualified by a MeSH qualifier
none
false
false
false
false
undefined_semantics
undefined_semantics
none
false
false
false
false
hasConcept
hasConcept
A MeSH description has a concept
none
false
false
false
false
undefined_semantics
undefined_semantics
none
false
false
false
false
hasPreferredConcept
hasPreferredConcept
A MeSH descriptor has a preferred concept
none
false
false
false
false
undefined_semantics
undefined_semantics
none
false
false
false
false
broader
broader than
one term is broader than another (SKOS?)
none
false
false
false
false
relatedTo
related to
none
false
false
false
false
narrower
narrower than
one term is narrower than another (SKOS?)
none
false
false
false
false
relatedTo
related to
none
false
false
false
false
related
related to
one term is related to another (SKOS?)
none
false
false
false
false
undefined_semantics
undefined_semantics
none
false
false
false
false
hasActivity
has activity
this thing exhibits that activity
none
false
false
false
false
undefined_semantics
undefined_semantics
none
false
false
false
false
terminates
terminates
Defines the relation of a terminator with a gene
terminated by
false
false
false
false
r
is related to
Root relation type
is related to
false
true
true
false
is_equivalent_to
is_equivalent_to
is_equivalent_to
false
true
true
true
physical
has_physical_relation_with
none
false
false
false
false
isfirstgeneof
First Gene Of
First Gene Of an FFL
hasfirstgene
true
false
false
false
r
is related to
Root relation type
is related to
false
true
true
false
issecondgeneof
Second Gene Of
Second Gene Of an FFL
hassecondgene
true
false
false
false
r
is related to
Root relation type
is related to
false
true
true
false
isthirdgeneof
Third Gene Of
Third Gene Of an FFL
hasthirdgene
true
false
false
false
r
is related to
Root relation type
is related to
false
true
true
false
max_expressed_in
Max Expressed In
Max Expressed In
maxexpresses
true
false
false
false
r
is related to
Root relation type
is related to
false
true
true
false
min_expressed_in
Min Expressed In
Min Expressed In
expressesmin
true
false
false
false
r
is related to
Root relation type
is related to
false
true
true
false