DAVID Bioinformatics 6.7
The Database for Annotation, Visualization and Integrated Discovery
DAVID Bioinformatics Resources 6.7
National Institute of Allergy and Infectious Diseases (NIAID), NIH
api

DAVID API


Comments and Suggestions!


Linking Methods



http://david.abcc.ncifcrf.gov/api.jsp?type=xxxxx&ids=XXXXX,XXXXX,XXXXXX,&tool=xxxx&annot=xxxxx,xxxxxx,xxxxx,




Some Limitations



  • DAVID APIs (alpha) allow other bioinformatics web sites to directly link to DAVID tools and functions ONLY for light-duty jobs (i.e. a gene list with no more than 400 genes).
  • DAVID APIs (alpha) are not for high-throughput or large gene list jobs, such as: a job for a gene list with more than 500 genes; try to loop DAVID data through scripts for hundreds/thousands of gene lists. For big jobs like above, you need to do them in a regular way through manual submission form on DAVID web site, or to download DAVID Knowledgebase to setup in-house analysis engines, or to contact DAVID team for alternative automatic solutions to meet you specific situations.
  • URL has a charactor size limitation (<= 2048 characters in total), i.e., the very large gene list may not be able to completely passed by URL.
  • No more than 200 hits in a day from one computer.
  • 10 seconds interval between hits.
  • DAVID Team reserves right to suspend any improper uses of DAVID APIs without notice.


Examples







Functional Annotation Summary Page



http://david.abcc.ncifcrf.gov/api.jsp?type=ENTREZ_GENE_ID&ids=2919,6347,6348,6364&tool=summary




Functional Annotation Chart



http://david.abcc.ncifcrf.gov/api.jsp?type=ENTREZ_GENE_ID&ids=2919,6347,6348,6364&tool=chartReport&annot=
GOTERM_BP_FAT,GOTERM_CC_FAT,GOTERM_MF_FAT,INTERPRO,PIR_SUPERFAMILY,SMART,BBID,BIOCARTA,
KEGG_PATHWAY,COG_ONTOLOGY,SP_PIR_KEYWORDS,UP_SEQ_FEATURE,GENETIC_ASSOCIATION_DB_DISEASE,OMIM_DISEASE




Functional Annotation Table



http://david.abcc.ncifcrf.gov/api.jsp?type=ENTREZ_GENE_ID&ids=2919,6347,6348,6364&tool=annotationReport&annot=
GOTERM_BP_FAT,GOTERM_CC_FAT,GOTERM_MF_FAT,INTERPRO,PIR_SUPERFAMILY,SMART,BBID,BIOCARTA,
KEGG_PATHWAY,COG_ONTOLOGY,SP_PIR_KEYWORDS,UP_SEQ_FEATURE,GENETIC_ASSOCIATION_DB_DISEASE,OMIM_DISEASE




Functional Annotation Clustering



http://david.abcc.ncifcrf.gov/api.jsp?type=ENTREZ_GENE_ID&ids=2919,6347,6348,6364&tool=term2term&annot=
GOTERM_BP_FAT,GOTERM_CC_FAT,GOTERM_MF_FAT,INTERPRO,PIR_SUPERFAMILY,SMART,BBID,
BIOCARTA,KEGG_PATHWAY,COG_ONTOLOGY,SP_PIR_KEYWORDS,UP_SEQ_FEATURE,GENETIC_ASSOCIATION_DB_DISEASE,
OMIM_DISEASE




Gene Full Report



http://david.abcc.ncifcrf.gov/api.jsp?type=ENTREZ_GENE_ID&ids=2919,6347,6348,6364&tool=geneReportFull




Gene Report



http://david.abcc.ncifcrf.gov/api.jsp?type=ENTREZ_GENE_ID&ids=2919,6347,6348,6364&tool=geneReport




Show Gene List Names in Batch



http://david.abcc.ncifcrf.gov/api.jsp?type=ENTREZ_GENE_ID&ids=2919,6347,6348,6364&tool=list




Gene Functional Classfication



http://david.abcc.ncifcrf.gov/api.jsp?type=ENTREZ_GENE_ID&ids=2919,6347,6348,6364&tool=gene2gene



Specification of Tag Values



For "tool" tag:


Valid Values
Corresponding DAVID Functions
gene2gene
term2term
summary
chartReport
annotationReport
list
geneReport
geneReportFull
Gene Functional Classification
Funtional Annotation Clustering
Functional Annotation Summary
Functional Annotation Chart
Functional Annotation Table
Show Gene List Names in Batch
Gene Report
Gene Full Report



For "type" tag:
Valid Values
 AFFYMETRIX_3PRIME_IVT_ID
 AFFYMETRIX_EXON_GENE_ID
 AFFYMETRIX_SNP_ID
 AGILENT_CHIP_ID
 AGILENT_ID
 AGILENT_OLIGO_ID
 ENSEMBL_GENE_ID
 ENSEMBL_TRANSCRIPT_ID
 ENTREZ_GENE_ID
 FLYBASE_GENE_ID
 FLYBASE_TRANSCRIPT_ID
 GENBANK_ACCESSION
 GENPEPT_ACCESSION
 GENOMIC_GI_ACCESSION
 PROTEIN_GI_ACCESSION
 ILLUMINA_ID
 IPI_ID
 MGI_ID
 GENE_SYMBOL
 PFAM_ID
 PIR_ACCESSION
 PIR_ID
 PIR_NREF_ID
 REFSEQ_GENOMIC
 REFSEQ_MRNA
 REFSEQ_PROTEIN
 REFSEQ_RNA
 RGD_ID
 SGD_ID
 TAIR_ID
 UCSC_GENE_ID
 UNIGENE
 UNIPROT_ACCESSION
 UNIPROT_ID
 UNIREF100_ID
 WORMBASE_GENE_ID
 WORMPEP_ID
 ZFIN_ID



For "annot" tag:
Valid Values
Category
GOTERM_BP_1
GOTERM_BP_2
GOTERM_BP_3
GOTERM_BP_4
GOTERM_BP_5
GOTERM_BP_ALL
GOTERM_BP_FAT
GOTERM_CC_1
GOTERM_CC_2
GOTERM_CC_3
GOTERM_CC_4
GOTERM_CC_5
GOTERM_CC_ALL
GOTERM_CC_FAT
GOTERM_MF_1
GOTERM_MF_2
GOTERM_MF_3
GOTERM_MF_4
GOTERM_MF_5
GOTERM_MF_ALL
GOTERM_MF_FAT
Gene_Ontology
BLOCKS_ID
COG
INTERPRO
PDB_ID
PFAM
PIR_ALN
PIR_HOMOLOGY_DOMAIN
PIR_SUPERFAMILY
PRINTS
PRODOM
PROSITE
SCOP_ID
SMART
TIGRFAMS
Protein_Domains
BBID
BIOCARTA
EC_NUMBER
KEGG_COMPOUND
KEGG_PATHWAY
KEGG_REACTION
Pathways
ALIAS_GENE_SYMBOL
CHROMOSOME
CYTOBAND
GENE
GENE_SYMBOL
HOMOLOGOUS_GENE
LL_SUMMARY
OMIM_ID
PIR_SUMMARY
PROTEIN_MW
REFSEQ_PRODUCT
SEQUENCE_LENGTH
SP_COMMENT
General Annotations
CGAP_EST_QUARTILE
CGAP_EST_RANK
COG_ONTOLOGY
PIR_SEQ_FEATURE
SP_COMMENT_TYPE
SP_PIR_KEYWORDS
UP_SEQ_FEATURE
Functional Categories
BIND
DIP
HIV_INTERACTION_CATEGORY
HIV_INTERACTION
MINT
NCICB_CAPATHWAY
TRANSFAC_ID
Protein-Protein Interaction
GENERIF_SUMMARY
HIV_INTERACTION_PUBMED_ID
PUBMED_ID
Literature
GENETIC_ASSOCIATION_DB_DISEASE
OMIM_DISEASE
Disease





 Please cite Nature Protocols 2009; 4(1):44 & Nucleic Acids Res. 2009;37(1):1 within any publication that makes use of any methods inspired by DAVID.
                          

        

                 
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