• Class Hierarchy
• Class definitions
• Instance definitions
• Slot definitions

Slots are inherited by a class from its parent classes. Usually this HTML form of the ontology shows only the names of the slots at each class, with links provided to the full definition of the slot in the slot section of the ontology. However, when the definition of a slot is changed within a class with respect to its parent, the full definition of the slot is shown.

Class: Databases

Instances: SGD-PATHWAY, ECHOBASE, PIRE, UNIPROT, CAS, NCBI-TAXONOMY-DB, ECOCYC, ECOGENE, BIOHEALTHBASE, UCSC, DBGET, UM-BBD-CPD, PUBCHEM, CGSC, ECOL199310CYC, WIT-PWY, PDB, MTBCDCCYC, HOMINISDB2, ENTREZ, GENECARDS, WIT, NRSUB, LIGAND-CPD, OU-MICROARRAY, SWISSPROT, NCI, ECOO157CYC, REFSEQ, TAIR, LIGAND, SHIGELLACYC, NCBI-GENE, LOCUSLINK, PUBMED, METACYC, UM-BBD-PWY, PYLORIGENE, MTBRVCYC, GO, SOYBASE, PID, UNIGENE, SWISSMODEL, SFLE198214CYC, SGD, ENZYME-DB, MIM, LIGAND-MAP, NEW-WIT-PWY, MPMP, HIDB, ENSEMBL, COLIBLAST, ECOLIHUB, CRYPTODB, HOMINISDB, CYRPTODB, ASAP, PFAM, HUMANCYC, PLASMOCYC, ECOLIWIKI, MODBASE, Wikipedia, CHEBI, BRENDA, ARACYC, INTERPRO, GI, KNAPSACK, REACTOME, SGN, PIR

Slots:

• ABBREV-NAME
• BASE-URL
• COMMENT
• COMMENT-INTERNAL
• COMMON-NAME: Databases
• CREDITS
• DATA-SOURCE
• HISTORY
• LINK-PREFIX-TEXT
• LOCAL-KB-ORGID
• NAMES
• PGDB?
• REGEXP
• SCHEMA?: T
• SEARCH-OBJECT-CLASS
• STATIC-SEARCH-URL
• SYNONYMS

Instance: SGD-PATHWAY

Slots:

• ABBREV-NAME: YeastCyc
• COMMENT: YeastCyc Saccharomyces Pathway Database
• COMMON-NAME: Saccharamyces Pathway Database
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Pathways
• STATIC-SEARCH-URL: http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=~A

Instance: ECHOBASE

Slots:

• ABBREV-NAME: EchoBASE
• BASE-URL: http://www.ecoli-york.org/
• COMMON-NAME: EchoBASE
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: All-Genes
• STATIC-SEARCH-URL: http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=~A

Instance: PIRE

Slots:

• BASE-URL: http://pir.georgetown.edu
• COMMENT: Link to an E. coli K-12 protein in PIR using the E. coli b-number of the gene (E. coli K-12 only)
• COMMON-NAME: PIR
• NAMES
• SCHEMA?
• STATIC-SEARCH-URL: http://pir.georgetown.edu/cgi-bin/nbrfget?xref=uwgp&~A

Instance: UNIPROT

Slots:

• ABBREV-NAME: UniProt
• BASE-URL: http://uniprot.org/
• COMMENT: The UniProt Knowledge Base has two component databases: SwissProt and TrEMBL.
• COMMON-NAME: UniProt
• NAMES
• REGEXP: ^(?:[A-NR-Z][0-9][A-Z][A-Z0-9]{2}[0-9])|(?:[OPQ][0-9][A-Z0-9]{3}[0-9])$
• SCHEMA?
• SEARCH-OBJECT-CLASS: Protein-Complexes, Polypeptides
• STATIC-SEARCH-URL: http://www.uniprot.org/uniprot/~A

Instance: CAS

Slots:

• ABBREV-NAME: CAS
• BASE-URL: http://www.cas.org/
• COMMENT: Chemical Abstract Service
• COMMON-NAME: CAS
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Compounds

Instance: NCBI-TAXONOMY-DB

Slots:

• ABBREV-NAME: NCBI-Taxonomy
• BASE-URL: http://www.ncbi.nlm.nih.gov/Taxonomy/
• COMMENT: NCBI database describing evolutionary taxonomy of organisms.
• COMMON-NAME: NCBI Taxonomy
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Organisms
• STATIC-SEARCH-URL: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=~A

Instance: ECOCYC

Slots:

• BASE-URL: http://biocyc.org
• COMMON-NAME: EcoCyc
• LOCAL-KB-ORGID: ECOLI
• NAMES
• PGDB?: T
• SCHEMA?
• SEARCH-OBJECT-CLASS: Compounds, Genes, Proteins, Reactions, Pathways
• STATIC-SEARCH-URL: http://biocyc.org/new-image?object=~A

Instance: ECOGENE

Slots:

• ABBREV-NAME: EcoGene
• BASE-URL: http://www.ecogene.org/
• COMMON-NAME: EcoGene
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Genes
• STATIC-SEARCH-URL: http://www.ecogene.org/geneInfo.php?eg_id=~A

Instance: BIOHEALTHBASE

Slots:

• ABBREV-NAME: BHB
• BASE-URL: http://www.biohealthbase.org
• COMMON-NAME: BioHealthBase
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Genes
• STATIC-SEARCH-URL: http://www.biohealthbase.org/GSearch/details.do?locus=~A

Instance: UCSC

Slots:

• ABBREV-NAME: UCSC Human
• BASE-URL: http://genome.ucsc.edu/
• COMMENT: This site at UCSC contains working drafts for the human, mouse, and rat genomes.
• COMMON-NAME: UCSC genome DB. Human
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: DNA-Segments
• STATIC-SEARCH-URL: http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=~A

Instance: DBGET

Slots:

• BASE-URL: http://www.genome.ad.jp/dbget/dbget.links.html
• SCHEMA?
• SEARCH-OBJECT-CLASS: Compounds, Polypeptides
• STATIC-SEARCH-URL: http://www.genome.ad.jp/dbget-bin/www_bget?~A

Instance: UM-BBD-CPD

Slots:

• ABBREV-NAME: UMBBD-Compounds
• BASE-URL: http://umbbd.ahc.umn.edu/
• COMMON-NAME: University of Minnesota Biocatalysis/Biodegradation Database - Compounds
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Compounds
• STATIC-SEARCH-URL: http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=c&compID=~A

Instance: PUBCHEM

Slots:

• ABBREV-NAME: PubChem
• BASE-URL: http://pubchem.ncbi.nlm.nih.gov/
• COMMON-NAME: PubChem
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Chemicals
• STATIC-SEARCH-URL: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=~A

Instance: CGSC

Slots:

• ABBREV-NAME: CGSC
• BASE-URL: http://cgsc.biology.yale.edu/top.html
• COMMENT: The Coli Genetic Stock Center at Yale.
• COMMON-NAME: Coli Genetic Stock Center
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Genes
• STATIC-SEARCH-URL: http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/~A

Instance: ECOL199310CYC

Slots:

• BASE-URL: http://BioCyc.org/
• COMMON-NAME: Ecol199310Cyc
• LOCAL-KB-ORGID: ECOL199310
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Proteins, Genes
• STATIC-SEARCH-URL: http://BioCyc.org/ECOL199310/new-image?object=~A

Instance: WIT-PWY

Slots:

• ABBREV-NAME: WIT
• BASE-URL: http://wit.mcs.anl.gov/WIT2
• COMMON-NAME: WIT-PWY
• NAMES
• SCHEMA?
• STATIC-SEARCH-URL: http://wit.mcs.anl.gov/WIT2/CGI/pw.cgi?pw=~A

Instance: PDB

Slots:

• ABBREV-NAME: PDB
• BASE-URL: http://www.rcsb.org/pdb/
• COMMON-NAME: Protein Data Bank
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Proteins
• STATIC-SEARCH-URL: http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=~A

Instance: MTBCDCCYC

Slots:

• COMMON-NAME: MtbCdcCyc
• LOCAL-KB-ORGID: MTBCDC
• NAMES
• SCHEMA?: NIL
• SEARCH-OBJECT-CLASS: Compounds, Genes, Proteins, Reactions, Pathways
• STATIC-SEARCH-URL: http://BioCyc.org/MTBCDC/new-image?object=~A

Instance: HOMINISDB2

Slots:

• ABBREV-NAME: CryptoDB, CDB
• BASE-URL: http://cryptodb.org
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Genes
• STATIC-SEARCH-URL: http://cryptodb.org/cryptodb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&id=~A

Instance: ENTREZ

Slots:

• ABBREV-NAME: Entrez-Nucleotide
• BASE-URL: http://www.ncbi.nlm.nih.gov/Entrez/
• COMMENT: We link to the Entrez Core Nucleotide database by primary accession number.
• COMMON-NAME: Entrez-Nucleotide
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: DNA-Segments
• STATIC-SEARCH-URL: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=~A

Instance: GENECARDS

Slots:

• ABBREV-NAME: GeneCards
• BASE-URL: http://bioinfo.weizmann.ac.il/cards/
• COMMENT: GeneCards[tm] is a database of human genes, their products and their involvement in diseases. It offers concise information about the functions of all human genes that have an approved symbol, as well as selected others.
• COMMON-NAME: GeneCards
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: DNA-Segments
• STATIC-SEARCH-URL: http://www.genecards.org/cgi-bin/carddisp.pl?gene=~A

Instance: WIT

Slots:

• BASE-URL: http://www.cme.msu.edu/WIT/
• COMMON-NAME: WIT
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: EC-Reactions
• STATIC-SEARCH-URL: http://www.cme.msu.edu/wit-cgi/wit_enzyme.cgi?~A

Instance: NRSUB

Slots:

• ABBREV-NAME: NRSub
• BASE-URL: http://acnuc.univ-lyon1.fr/nrsub/nrsub.html
• COMMON-NAME: Non-Redundant Bacillus subtilis database
• NAMES
• SCHEMA?
• STATIC-SEARCH-URL: http://acnuc.univ-lyon1.fr/cgi-bin/acnuc-search-bg?query=~A

Instance: LIGAND-CPD

Slots:

• BASE-URL: http://www.genome.ad.jp/dbget/ligand.html
• COMMON-NAME: LIGAND
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Compounds
• STATIC-SEARCH-URL: http://www.genome.ad.jp/dbget-bin/www_bget?compound+~A

Instance: OU-MICROARRAY

Slots:

• BASE-URL: http://www.ou.edu/microarray
• COMMON-NAME: OUMCF
• LINK-PREFIX-TEXT: See microarray expression data for this gene:
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Genes
• STATIC-SEARCH-URL: http://chase.ou.edu/oubcf/index.php?bnum=~A

Instance: SWISSPROT

Slots:

• BASE-URL: http://www.expasy.ch/sprot/sprot-top.html
• COMMENT: Technically, Swiss-Prot is a subset of UniProt. It is preferable to link using the DBID UNIPROT, because linking via DBID SWISSPROT assumes we know that a protein is in SwissProt as opposed to TrEMBL. DBID SWISSPROT is provided for backward compatibility with earlier BioCyc links that use that DBID. Because even in the existing links it is possible that some links are really to TrEMBL, I have changed the Common-Name slot in this frame to be UniProtKB (PDK).
• COMMON-NAME: UniProtKB
• NAMES
• SCHEMA?
• STATIC-SEARCH-URL: http://www.expasy.ch/cgi-bin/sprot-search-ac?~A

Instance: NCI

Slots:

• ABBREV-NAME: NCI
• COMMENT: The ID required for this dblink to work is the NSC number, and only the number, without any prefix letters.
• COMMON-NAME: NCI Open DB
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Compounds
• STATIC-SEARCH-URL: http://cactus.nci.nih.gov/ncidb2/?nsc=~A

Instance: ECOO157CYC

Slots:

• BASE-URL: http://BioCyc.org/
• COMMON-NAME: EcoO157Cyc
• LOCAL-KB-ORGID: ECOO157
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Proteins, Genes
• STATIC-SEARCH-URL: http://BioCyc.org/ECOO157/new-image?object=~A

Instance: REFSEQ

Slots:

• ABBREV-NAME: RefSeq
• BASE-URL: http://www.ncbi.nih.gov/RefSeq/
• COMMENT: The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for major research organisms.
• COMMON-NAME: NCBI Reference Sequences Database
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Polypeptides, Genes
• STATIC-SEARCH-URL: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=~A

Instance: TAIR

Slots:

• ABBREV-NAME: TAIR
• BASE-URL: http://www.arabidopsis.org/
• COMMON-NAME: The Arabidopsis Information Resource
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Genes
• STATIC-SEARCH-URL: http://www.arabidopsis.org/servlets/TairObject?type=locus&name=~A

Instance: LIGAND

Slots:

• BASE-URL: http://www.genome.ad.jp/dbget/ligand.html
• COMMON-NAME: LIGAND
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: EC-Reactions
• STATIC-SEARCH-URL: http://www.genome.ad.jp/dbget-bin/www_bget?ligand+~A

Instance: SHIGELLACYC

Slots:

• BASE-URL: http://BioCyc.org/
• COMMON-NAME: ShigellaCyc
• LOCAL-KB-ORGID: SHIGELLA
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Proteins, Genes
• STATIC-SEARCH-URL: http://BioCyc.org/SHIGELLA/new-image?object=~A

Instance: NCBI-GENE

Slots:

• ABBREV-NAME: Entrez-gene
• COMMENT: The Entrez-Gene Database allows reference to individual genes that were sequenced as part of a genome sequencing project. The accession number of the genes in the database is referred to as a Gene ID. When references to Gene IDs are included in the annotated genome of an organism, the PathoLogic component of Pathway Tools will create links to this database during the generation of the PGDB.
• COMMON-NAME: Entrez-Gene
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Genes, DNA-Segments
• STATIC-SEARCH-URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&list_uids=~A

Instance: LOCUSLINK

Slots:

• ABBREV-NAME: LocusLink
• BASE-URL: http://www.ncbi.nlm.nih.gov/LocusLink/
• COMMENT: NCBI database of genetic loci
• COMMON-NAME: NCBI LocusLink
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: DNA-Segments
• STATIC-SEARCH-URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=summary&list_uids=~A

Instance: PUBMED

Slots:

• BASE-URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
• SCHEMA?
• STATIC-SEARCH-URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=~A&dopt=Abstract

Instance: METACYC

Slots:

• BASE-URL: http://biocyc.org
• COMMON-NAME: MetaCyc
• LOCAL-KB-ORGID: META
• NAMES
• PGDB?: T
• SCHEMA?
• SEARCH-OBJECT-CLASS: Proteins, Compounds, Reactions, Genes, Pathways
• STATIC-SEARCH-URL: http://biocyc.org/META/new-image?object=~A

Instance: UM-BBD-PWY

Slots:

• ABBREV-NAME: UMBBD-Pathways
• BASE-URL: http://umbbd.ahc.umn.edu/
• COMMON-NAME: University of Minnesota Biocatalysis/Biodegradation Database - Pathways
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Pathways
• STATIC-SEARCH-URL: http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=p&pathway_abbr=~A

Instance: PYLORIGENE

Slots:

• BASE-URL: http://genolist.pasteur.fr/PyloriGene
• COMMON-NAME: PyloriGene
• INTERNAL-COMMENT: STATIC-SEARCH-URL generates an error in Netscape Communicator 4.79 for Solaris. Test the URL on another web browser
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Genes
• STATIC-SEARCH-URL: http://genolist.pasteur.fr/PyloriGene/genome.cgi?external_query+~A

Instance: MTBRVCYC

Slots:

• COMMON-NAME: MtbRvCyc
• LOCAL-KB-ORGID: MTBRV
• NAMES
• SCHEMA?: NIL
• SEARCH-OBJECT-CLASS: Compounds, Genes, Proteins, Reactions, Pathways
• STATIC-SEARCH-URL: http://BioCyc.org/MTBRV/new-image?object=~A

Instance: GO

Slots:

• ABBREV-NAME: GO
• BASE-URL: http://www.geneontology.org/
• COMMENT: The objective of GO is to provide controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products.
• COMMON-NAME: Gene Ontology Database
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Proteins, Genes
• STATIC-SEARCH-URL: http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?query=~A&search_constraint=terms&action=query&view=query

Instance: SOYBASE

Slots:

• BASE-URL: http://soybase.agron.iastate.edu/
• COMMON-NAME: Soybase
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Pathways
• STATIC-SEARCH-URL: http://soybase.ncgr.org/cgi-bin/ace/generic/pic/soybase?class=Reaction_or_Pathway&name=%21~A

Instance: PID

Slots:

• ABBREV-NAME: Entrez
• BASE-URL: http://www.ncbi.nlm.nih.gov/Entrez/protein.html
• COMMENT: Entrez protein database. Created because 'PID' is the string used in annotation.
• COMMON-NAME: Entrez Protein Sequence
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Proteins
• STATIC-SEARCH-URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein&cmd=Search&term=~A&doptcmdl=GenPept

Instance: UNIGENE

Slots:

• ABBREV-NAME: UniGene
• BASE-URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene
• COMMENT: UniGene is an experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters. Each UniGene cluster contains sequences that represent a unique gene, as well as related information such as the tissue types in which the gene has been expressed and map location.
• COMMON-NAME: NCBI UniGene (Homo sapiens)
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: DNA-Segments
• STATIC-SEARCH-URL: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=~A

Instance: SWISSMODEL

Slots:

• BASE-URL: http://swissmodel.expasy.org/repository/
• COMMON-NAME: Swiss-Model
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Polypeptides
• STATIC-SEARCH-URL: http://swissmodel.expasy.org/repository/smr.php?sptr_ac=~A&job=2

Instance: SFLE198214CYC

Slots:

• BASE-URL: http://BioCyc.org/
• COMMON-NAME: Sfle198214Cyc
• LOCAL-KB-ORGID: SFLE198214
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Proteins, Genes
• STATIC-SEARCH-URL: http://BioCyc.org/SFLE198214/new-image?object=~A

Instance: SGD

Slots:

• ABBREV-NAME: SGD
• COMMENT: SacchDB Yeast DB at Stanford
• COMMON-NAME: Saccharamyces Gene Database
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: DNA-Segments
• STATIC-SEARCH-URL: http://db.yeastgenome.org/cgi-bin/locus.pl?locus=~A

Instance: ENZYME-DB

Slots:

• BASE-URL: http://www.expasy.ch/sprot/enzyme.html
• COMMON-NAME: ENZYME
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: EC-Reactions
• STATIC-SEARCH-URL: http://ca.expasy.org/cgi-bin/nicezyme.pl?~A

Instance: MIM

Slots:

• ABBREV-NAME: OMIM
• BASE-URL: http://www.ncbi.nlm.nih.gov/omim/
• COMMENT: This database is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for Biotechnology Information.
• COMMON-NAME: Online Mendelian Inheritance in Man
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Genes
• STATIC-SEARCH-URL: http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=~A

Instance: LIGAND-MAP

Slots:

• ABBREV-NAME: LIGAND
• BASE-URL: http://www.genome.ad.jp/dbget/ligand.html
• COMMON-NAME: LIGAND-MAP
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Pathways
• STATIC-SEARCH-URL: http://www.genome.ad.jp/dbget-bin/show_pathway?~A

Instance: NEW-WIT-PWY

Slots:

• BASE-URL: http://wit.mcs.anl.gov/WIT2/wit.html
• COMMON-NAME: WIT-PWY
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Pathways
• STATIC-SEARCH-URL: http://wit.mcs.anl.gov/WIT/CGI/pw.cgi?compare=&pw=~A&org=&user=&where=show_diagram

Instance: MPMP

Slots:

• BASE-URL: http://sites.huji.ac.il/malaria/
• SCHEMA?
• STATIC-SEARCH-URL: http://sites.huji.ac.il/malaria/maps/~A.html

Instance: HIDB

Slots:

• BASE-URL: http://www.tigr.org/tdb/mdb/hidb/hidb.html
• COMMON-NAME: HIDB
• NAMES
• SCHEMA?
• STATIC-SEARCH-URL: http://www.tigr.org/docs/tigr-scripts/hi_scripts/hi_report.spl?hi_num=~A

Instance: ENSEMBL

Slots:

• ABBREV-NAME: Ensembl
• BASE-URL: http://www.ensembl.org/Homo_sapiens/
• COMMENT: Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on eukaryotic genomes.
• COMMON-NAME: Ensembl Human
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: DNA-Segments
• STATIC-SEARCH-URL: http://www.ensembl.org/Homo_sapiens/Gene/Idhistory?g=~A

Instance: COLIBLAST

Slots:

• COMMENT: This is not exactly a database; it is a collection of files that contain blast reports from the comparision of H.inf genes to E. coli genes.
• COMMON-NAME: ColiBlast
• NAMES
• SCHEMA?
• STATIC-SEARCH-URL: http://www.ai.sri.com/cgi-bin/sb/blast2html.pl.cgi?filename=~A

Instance: ECOLIHUB

Slots:

• BASE-URL: http://www.ecolicommunity.org:8348/EcoliHub/
• COMMON-NAME: EcoliHub
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Genes
• STATIC-SEARCH-URL: http://www.ecolicommunity.org:8348/EcoliHub/remoteObject.do?namespace=tag_mg1655&namespace_id=~A&object=gene&datasource=genobase&displayMode=detailed_tabs

Instance: CRYPTODB

Slots:

• ABBREV-NAME: CryptoDB, CDB
• BASE-URL: http://cryptodb.org
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Genes
• STATIC-SEARCH-URL: http://cryptodb.org/cryptodb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&id=~A

Instance: HOMINISDB

Slots:

• ABBREV-NAME: CryptoDB, CDB
• BASE-URL: http://cryptodb.org
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Genes
• STATIC-SEARCH-URL: http://cryptodb.org/cryptodb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&id=~A

Instance: CYRPTODB

Slots:

• ABBREV-NAME: CryptoDB, CDB
• BASE-URL: http://cryptodb.org
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Genes
• STATIC-SEARCH-URL: http://cryptodb.org/cryptodb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&id=~A

Instance: ASAP

Slots:

• ABBREV-NAME: ASAP
• BASE-URL: http://asap.ahabs.wisc.edu/asap/home.php
• COMMENT:
• COMMON-NAME: ASAP
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Genes
• STATIC-SEARCH-URL: http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=~A

Instance: PFAM

Slots:

• ABBREV-NAME: Pfam
• BASE-SEARCH-URL: http://pfam.sanger.ac.uk
• BASE-URL: http://www.sanger.ac.uk/Software/Pfam/
• COMMENT: The Pfam collection of multiple sequence alignments and hidden Markov models for common protein families and domains.
• COMMON-NAME: Pfam
• NAMES
• PGDB?: NIL
• SCHEMA?
• SEARCH-OBJECT-CLASS: Polypeptides
• STATIC-SEARCH-URL: http://pfam.sanger.ac.uk/family?entry=~A&type=Family

Instance: HUMANCYC

Slots:

• ABBREV-NAME: HumanCyc
• COMMENT: Homo sapiens pathway database
• COMMON-NAME: HumanCyc
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Pathways
• STATIC-SEARCH-URL: http://biocyc.org/HUMAN/NEW-IMAGE?type=PATHWAY&object=~A

Instance: PLASMOCYC

Slots:

• ABBREV-NAME: PlasmoCyc
• COMMENT: Plasmodium falciparum Pathway Database
• COMMON-NAME: Plasmodium falciparum Pathway Database
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Pathways
• STATIC-SEARCH-URL: http://biocyc.org/PLASMO/NEW-IMAGE?type=PATHWAY&object=~A

Instance: ECOLIWIKI

Slots:

• BASE-URL: http://ecoliwiki.net/colipedia/index.php/Welcome_to_EcoliWiki
• COMMENT: The EcoliWiki is EcoliHub's subsystem for community annotation.
• COMMON-NAME: EcoliWiki
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Polypeptides, RNA
• STATIC-SEARCH-URL: http://ecoliwiki.net/colipedia/index.php/~A

Instance: MODBASE

Slots:

• ABBREV-NAME: ModBase
• BASE-URL: http://salilab.org/modbase/
• COMMENT: MODBASE is a database of predicted protein 3-D structures developed by the Sali lab at UCSF.
• COMMON-NAME: MODBASE
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Polypeptides
• STATIC-SEARCH-URL: http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchkw=name&kword=~A

Instance: Wikipedia

Slots:

• ABBREV-NAME: Wikipedia
• BASE-URL: http://en.wikipedia.org/
• COMMENT: Wikipedia is a multilingual, web-based, free content encyclopedia project, which is written collaboratively by volunteers from all around the world.
• COMMON-NAME: Wikipedia
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Compounds, Pathways, RNA, Protein-Complexes, Polypeptides, Genes
• STATIC-SEARCH-URL: http://en.wikipedia.org/wiki/~A

Instance: CHEBI

Slots:

• ABBREV-NAME: ChEBI
• BASE-URL: http://www.ebi.ac.uk/chebi/
• COMMENT: Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.
• COMMON-NAME: ChEBI
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Compounds
• STATIC-SEARCH-URL: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:~A

Instance: BRENDA

Slots:

• BASE-URL: http://www.brenda-enzymes.info
• COMMON-NAME: BRENDA
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Reactions
• STATIC-SEARCH-URL: http://www.brenda-enzymes.info/php/result_flat.php4?ecno=~A

Instance: ARACYC

Slots:

• BASE-URL: http://www.arabidopsis.org/
• COMMON-NAME: AraCyc
• LOCAL-KB-ORGID: ARA
• NAMES
• PGDB?: T
• SCHEMA?
• SEARCH-OBJECT-CLASS: Pathways
• STATIC-SEARCH-URL: http://www.arabidopsis.org:1555/ARA/NEW-IMAGE?type=PATHWAY&object=~A

Instance: INTERPRO

Slots:

• COMMENT: InterPro is an integrated documentation resource for protein families, domains and sites.
• COMMON-NAME: InterPro
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Polypeptides, Genes
• STATIC-SEARCH-URL: http://www.ebi.ac.uk/interpro/IEntry?ac=~A

Instance: GI

Slots:

• COMMENT: GI (Gene Index) is an older convention, still in use in Genbank protein entries, and is often found in genome annotations.
• COMMON-NAME: Entrez Protein (GI)
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Polypeptides, Genes
• STATIC-SEARCH-URL: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=~A

Instance: KNAPSACK

Slots:

• BASE-URL: http://kanaya.aist-nara.ac.jp/KNApSAcK/
• COMMENT: KNApSAcK is a species-metabolite relation database provided by the Nara Institute of Science and Technology (NAIST).
• COMMON-NAME: KNApSAcK
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Compounds
• STATIC-SEARCH-URL: http://kanaya.naist.jp/knapsack_jsp/information.jsp?sname=C_ID&word=~A

Instance: REACTOME

Slots:

• BASE-URL: http://www.reactome.org/
• COMMON-NAME: Reactome
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Pathways
• STATIC-SEARCH-URL: http://www.reactome.org/cgi-bin/link?SOURCE=Reactome&ID=~A

Instance: SGN

Slots:

• ABBREV-NAME: SGN
• BASE-URL: http://www.sgn.cornell.edu/
• COMMON-NAME: Sol Genomics Network
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Genes
• STATIC-SEARCH-URL: http://www.sgn.cornell.edu/search/unigene.pl?unigene_id=~A

Instance: PIR

Slots:

• BASE-URL: http://pir.georgetown.edu
• COMMENT: Link to a protein in PIR by the PIR id.
• COMMON-NAME: PIR
• NAMES
• SCHEMA?
• SEARCH-OBJECT-CLASS: Proteins
• STATIC-SEARCH-URL: http://www.pir.uniprot.org/cgi-bin/searchpsd?id=~A

Slot Name	Documentation	Properties
ABBREV-NAME	An abbreviated name for the current frame. This slot can be used for virtually all classes; see specification of the :Synonym-Slots for a given class to be sure. In particular, this name for a database is displayed in DB-links, and in some author credit displays of an organization's name.	DOMAIN: Compounds, Organizations, Databases VALUE-TYPE: STRING INHERITANCE-TYPE: UNIQUE MAXIMUM-CARDINALITY: 1 COMMON-NAME: Abbreviated-Name
BASE-URL	Stores URL for Database home page	DOMAIN: Databases VALUE-TYPE: STRING COMMON-NAME: Base-URL
COMMENT	The Comment slot stores a general comment about the object that contains the slot.	QUERYABLE?: T DOMAIN: THING VALUE-TYPE: STRING INHERITANCE-TYPE: UNIQUE COMMON-NAME: Comment
COMMENT-INTERNAL	A comment for internal purposes that is not released to the public.	DOMAIN: THING VALUE-TYPE: STRING INHERITANCE-TYPE: UNIQUE PRIVATE?: T COMMON-NAME: Comment-Internal
COMMON-NAME	The primary name by which an object is known to scientists -- a widely used and familiar name (in some cases arbitrary choices must be made).	QUERYABLE?: T DOMAIN: SLOTS, THING VALUE-TYPE: STRING INHERITANCE-TYPE: UNIQUE MAXIMUM-CARDINALITY: 1 COMMON-NAME: Common-Name
CREDITS	This slot attributes credit to various contributors, which can be individual people or organizations, or both. The type of contribution is indicated by several types of annotation labels that are attached to the slot values, each of them bearing numerical time-stamps as the values (in Common Lisp universal time format) that indicate the approximate times of the contributions. The code dealing with author-crediting sets and shows the timestamps with a precision of one day. The legal slot values are frames of the |People| or |Organizations| classes, in any combination or order. Each such contributor frame is assumed to occur only once in the slot. As of Oct. 2005, the legal annotation labels are: CREATED REVIEWED REVISED LAST-CURATED . For the annotation labels CREATED and LAST-CURATED , it only makes sense to store one timestamp, but for the other labels, in general, arbitrarily many timestamps can be recorded. An association between authors and organizations is assumed if they share the same credit event, in terms of the same combination of annotation label and timestamp.	QUERYABLE?: T DOMAIN: THING VALUE-TYPE: (OR People Organizations) INVERSE: CREDITED-FOR INHERITANCE-TYPE: UNIQUE COMMON-NAME: Credits
DATA-SOURCE	A string describing the data source from which this object was derived, such as the name of a laboratory or a database. Used principally by the PTools BioPAX importer.	QUERYABLE?: T DOMAIN: THING VALUE-TYPE: STRING INHERITANCE-TYPE: UNIQUE COMMON-NAME: Data-Source
HISTORY	Contains a textual history of changes made to this frame. Each item is either a string or a note frame.	DOMAIN: THING VALUE-TYPE: (OR STRING Notes) INVERSE: REFERENT-FRAMES INHERITANCE-TYPE: UNIQUE COLLECTION-TYPE: LIST COMMON-NAME: History
LINK-PREFIX-TEXT	This slot contains an optional string that the Navigator should display before every link to this database.	DOMAIN: Databases VALUE-TYPE: STRING MAXIMUM-CARDINALITY: 1 COMMON-NAME: Link-Prefix-Text
LOCAL-KB-ORGID	The Pathway Tools orgid for databases that are Pathway/Genome Databases (e.g. META for MetaCyc, ECOLI for EcoCyc).	DOMAIN: Databases VALUE-TYPE: SYMBOL COMMON-NAME: Local-KB-OrgID
NAMES	This is a computed slot that returns the union of all names of this frame, by appending names from all other name slots.	QUERYABLE?: T DOMAIN: Polymer-Segments, Organisms, Generalized-Reactions, Enzymatic-Reactions, Chemicals, Databases VALUE-TYPE: STRING GET-METHODS: GET-NAMES READ-ONLY: T COMMON-NAME: Names
PGDB?	True if the database is a Pathway/Genome Database that uses the Pathway Tools schema.	DOMAIN: Databases VALUE-TYPE: BOOLEAN CARDINALITY: 1 COMMON-NAME: PGDB?
REGEXP	This slot contains a regular expression string defining legal values for links to this database. The regular expression syntax is mostly compatible with Perl regular expression syntax, and is described at http://franz.com/support/documentation/8.1/doc/regexp.htm#regexp-new-summary-2.	DOMAIN: Databases VALUE-TYPE: STRING
SCHEMA?	This slot is used to indicate which KB classes are logically part of the general GenoPath (MetaCyc) schema (are organism-independent), in contrast to those classes that are specific to a particular organism. This slot is used by the PathoLogic code that does schema copying, and by the code in kb-update.lisp that does schema mirroring. The general rule is that classes that should be copied from MetaCyc to a new organism by PathoLogic are considered schema classes. Examples include the hierarchies of compounds and pathways, and general classes like Genes and Proteins and All-ACPs. Examples of classes to exclude are classes for specific modified proteins that occur as substrates in reactions, such as Thioredoxin. The problem with copying Theoredoxin is that the reactions it appears as a substrate in are not copied when the class is copied, causing bad references to those reactions.	DOMAIN: THING VALUE-TYPE: BOOLEAN INHERITANCE-TYPE: OVERRIDE MAXIMUM-CARDINALITY: 1 COMMON-NAME: Schema?
SEARCH-OBJECT-CLASS	This slot lists the classes of PGDB objects (e.g. Pathways, Genes, Proteins, etc.) that can have unification links to this database via the search URL.	DOMAIN: Databases VALUE-TYPE: THING COMMON-NAME: Search-Object-Class
STATIC-SEARCH-URL	Stores URL format string for OID searches. Format string has one arg: the desired OID.	DOMAIN: Databases VALUE-TYPE: STRING COMMON-NAME: Static-Search-URL
SYNONYMS	One or more secondary names for an object -- names that a scientist might attempt to use to retrieve the object. The Synonyms should include any name a user might use to try to retrieve an object.	QUERYABLE?: T DOMAIN: THING VALUE-TYPE: STRING INHERITANCE-TYPE: UNIQUE COMMON-NAME: Synonyms