api
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DAVID
API
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Comments and Suggestions!
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Linking Methods
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http://david.abcc.ncifcrf.gov/api.jsp?type=xxxxx&ids=XXXXX,XXXXX,XXXXXX,&tool=xxxx&annot=xxxxx,xxxxxx,xxxxx, |
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Some Limitations
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- 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.
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Examples
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Functional Annotation Summary
Page
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http://david.abcc.ncifcrf.gov/api.jsp?type=ENTREZ_GENE_ID&ids=2919,6347,6348,6364&tool=summary
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Functional Annotation Chart
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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
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Functional Annotation Table
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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
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Functional Annotation Clustering
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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
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Gene Full Report
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http://david.abcc.ncifcrf.gov/api.jsp?type=ENTREZ_GENE_ID&ids=2919,6347,6348,6364&tool=geneReportFull
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Gene Report
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http://david.abcc.ncifcrf.gov/api.jsp?type=ENTREZ_GENE_ID&ids=2919,6347,6348,6364&tool=geneReport
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Show Gene List Names in Batch
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http://david.abcc.ncifcrf.gov/api.jsp?type=ENTREZ_GENE_ID&ids=2919,6347,6348,6364&tool=list
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Gene Functional Classfication
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http://david.abcc.ncifcrf.gov/api.jsp?type=ENTREZ_GENE_ID&ids=2919,6347,6348,6364&tool=gene2gene
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Specification of Tag Values
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For "tool"
tag:
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Valid Values
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Corresponding DAVID
Functions
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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 |
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For
"type" tag:
Valid Values
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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
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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 |
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Gene_Ontology
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| BLOCKS_ID |
| COG |
| INTERPRO |
| PDB_ID |
| PFAM |
| PIR_ALN |
| PIR_HOMOLOGY_DOMAIN |
| PIR_SUPERFAMILY |
| PRINTS |
| PRODOM |
| PROSITE |
| SCOP_ID |
| SMART |
| TIGRFAMS |
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Protein_Domains
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| BBID |
| BIOCARTA |
| EC_NUMBER |
| KEGG_COMPOUND |
| KEGG_PATHWAY |
| KEGG_REACTION |
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Pathways
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| ALIAS_GENE_SYMBOL |
| CHROMOSOME |
| CYTOBAND |
| GENE |
| GENE_SYMBOL |
| HOMOLOGOUS_GENE |
| LL_SUMMARY |
| OMIM_ID |
| PIR_SUMMARY |
| PROTEIN_MW |
| REFSEQ_PRODUCT |
| SEQUENCE_LENGTH |
| SP_COMMENT |
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General Annotations
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| CGAP_EST_QUARTILE |
| CGAP_EST_RANK |
| COG_ONTOLOGY |
| PIR_SEQ_FEATURE |
| SP_COMMENT_TYPE |
| SP_PIR_KEYWORDS |
| UP_SEQ_FEATURE |
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Functional Categories
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| BIND |
| DIP |
| HIV_INTERACTION_CATEGORY |
| HIV_INTERACTION |
| MINT |
| NCICB_CAPATHWAY |
| TRANSFAC_ID |
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Protein-Protein Interaction
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| GENERIF_SUMMARY |
| HIV_INTERACTION_PUBMED_ID |
| PUBMED_ID |
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Literature
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| GENETIC_ASSOCIATION_DB_DISEASE |
| OMIM_DISEASE |
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Disease
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