Version 3
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This mirror
was last updated on
06/29/2011
Output File Format
This page provides information about the format of the output file supplied by the GeneALaCart Batch Queries engine of GeneCards.
- The development of the engine is still in progress. Therefore, some of the features are disabled and will be supplied in future versions.
- Current input consists of gene cards symbols, gene cards symbols/aliases or an assortment of symbols and other identifiers (UniProt, Ensembl, Entrez Gene, Hgnc, Aliases and/or GeneCards IDs). Symbols should be separated by white space separators only (space, tab or carriage return).
- You can enter your genes by pasting them or uploading a file. It is possible to choose the name for your output file.
- If a gene was not found in our database, the comment "NOT FOUND" will appear in the Gene Name field in the output file.
- By default, if your input contains more than one identifier for the same gene, it will appear only once in the output, with the redundancy noted. To preserve the order of entries (including unmatched) in the result list, the 'preserve original input file order' output file option (at the top of the page) should be selected.
- The symbol checkbox cannot be unchecked.
- At least one field, aside from the symbol, must be selected.
- Fields that do not contain information for this gene are left blank. In the case of the chromosome or the strand fields "NA" stands for 'no information is available'.
- Results are sent via email for large batches (over 250 genes) or when querying by uploading a file.
Output format and separators:
- Fields are separated by tabs
- List Items are separated by pipes (|)
- Information on items is separated from the items by the sharp symbol (#)
- Nested list items are separated by double pipes (||)
Example of a complex field output:
Allele1: MGI_id1#Phenotypes: |Allele2: MGI_id2#Phenotypes: phenotype_id1#phenotype_name||phenotype_id2#phenotype_name...
The fields that are currently available to be downloaded are the following (other fields will be available in future versions):
GeneCards section Queried fields Sources Gene Symbol HGNC, NCBI, Ensembl GeneCards ID GeneCards ID GeneCards, GeneLoc Category Category Entrez Gene, Ensembl, GeneCards Gene Description HGNC, Entrez Gene Approval Approved, Not approved HGNC Source HGNC, Entrez Gene, Ensembl GeneCards Inferred Functionality Scores GIFtS All GeneCards sources Aliases and Descriptions Aliases, Descriptions, External IDs HGNC, UniProtKB, SwissProt, TrEMBL, NCBI, OMIM, GeneLoc, Ensembl Summaries EntrezGene, UniProtKB, Tocris EntrezGene, UniProtKB/Swiss-Prot, Tocris Genomic Views Chromosome, strand, cytogenetic band, genomic location start/end, gene size, Mapped to contig (flag if the information is not genomic) GeneLoc, NCBI, Ensembl, Entrez Gene, HGNC, HORDE, miRBase Proteins Aliases, UniProtKB ID, protein name, size, cofactor, subunit, subcellular location, tissue specificity, developmental stage, ptm, miscellaneous, RefSeq ID, Ensembl ID UniProtKB, Entrez Gene(NCBI), Ensembl Protein Domains / Families InterPro domains, UniProtKB ID, UniProtKB domains, UniProtKB similarities EBI, UniProtKB Gene Function UniProtKB ID, UniProtKB function, MGI mutant phenotype UniProtKB, MGI Ontologies GO ID, GO term GO Pathways and Interactions EMD Millipore ID, EMD Millipore pathway description, Sigma-Aldrich summary ID, Sigma-Aldrich ID, Sigma-Aldrich pathway description, CST(Cell Signaling Technology) ID, CST pathway description, KEGG ID, KEGG pathway description EMD Millipore, Sigma-Aldrich, CST, KEGG Tocris compounds Compound name, Compound action, Compound CAS number Tocris HMDB compounds Compound name, synonyms, compound CAS number, pubmed Ids HMDB DrugBank compounds Compound name, synonyms, compound CAS number, type, actions, pubmed Ids DrugBank Novoseek compounds Compound name Novoseek PharmGKB compounds Compound name, Relations, PumMed IDs PharmGKB TarThera compounds Compound name TarThera Transcripts Refseq transcripts, Unigene cluster, Unigene cluster description RefSeq, Unigene Expression in Human tissues U95 probe-sets, binary expression patterns in tissues ordered as in the GeneCards display, sensitivity, specificity GeneNote, GeneAnnot Orthologs Organism, gene, percent protein similarity to the human gene, percent nucleotide similarity to the human gene HomoloGene, euGenes, MGI, SGD HomoloGene Paralogs gene HomoloGene Ensembl Paralogs gene Ensembl Genomic Variants number of NCBI snps, NCBI ID, location type, minor allele frequency, sample size, populations studied, validation, position, nucleotide change, amino acid change, sequence, number of sources NCBI OMIM disorders OMIM ID, Disorder ID OMIM UniProtKB disorders UniProtKB ID, Disorder description UniProtKB Novoseek disorders Disorder description Novoseek PharmGKB disorders Disorder description, Relations, PubMed IDs PharmGKB TarThera disorders Disorder description TarThera Publications PubMed IDs PubMed
Field formats
GeneCards_ID
gc_id
Category
protein-coding,
pseudogene, RNA gene, genetic locus,
gene cluster, or uncategorized
Gene Description
Gene description according to HGNC or Entrez Gene
Approval
Approved, not approved according to HGNC
Source
Gene symbol from HGNC, Entrez Gene or Ensembl
GIFtS
An integer that represents the GeneCards Inferred Functionality Score
Aliases and Descriptions
alias1 or description1|alias2 or description2|alias3 or description3|...
External IDs
entrezgene_id|ensembl_id|hgnc_id|
EntrezGene summary
Summary from EntrezGene
UniProtKB/Swiss-Prot summary
Function1|Function2|Function3|...
Tocris summary
Summary from Tocris
Chromosome
1-22 or X,Y,MT (mitochondria). NA appears where chromosome is unknown.
Strand
Plus, Minus or NA (where strand is unknown)
Cytogenetic band
Cytogenetic band according to Entrez Gene, Ensembl and/or HGNC
Gene start
Chromosomal coordinate in bp from pter
Gene end
Chromosomal coordinate in bp from pter
Gene size
Size of genomic sequence in bp
UniProtKB Protein details
source:aliases|uniprotkb protein_id1#protein name#size#cofactor & cofactor#subunit & subunit#subcellular location & subcellular location#tissue specificity & tissue specificity#
developmental stage & developmental stage#ptm & ptm#miscellaneous & miscellaneous|
uniprotkb protein_id2#protein name#size#cofactor..#subunit..#subcellular location..#tissue specificity..#developmental stage..#ptm..#miscellaneous..|
uniprotkb protein_id3#protein name#size#cofactor..#subunit..#subcellular location..#tissue specificity..#developmental stage..#ptm..#miscellaneous..|...
RefSeq Protein ID
refseq protein_id1|refseq protein_id2|refseq protein_id3|...
Ensembl Protein ID
ensembl protein_id1|ensembl protein_id2|ensembl protein_id3|...
InterPro domains and families
InterPro_id1#domain_name|InterPro_id2#domain_name...
UniProtKB Domains and Families
source:uniprotkb_id1#domain & domain..#similarity & similarity..|uniprotkb_id2#domain & domain..#similarity & similarity..|uniprotkb_id3#domain & domain..#similarity & similarity..|...
Gene Function - UniProtKB
source:uniprotkb_id1#function|uniprotkb_id2#function|uniprotkb_id3#function...
Gene Function - MGI mutant phenotype
Allele1: MGI_id1#Phenotypes: |Allele2: MGI_id2#Phenotypes: phenotype_id1#phenotype_name||phenotype_id2#phenotype_name...
Gene Ontologies (GO)
go_id1#go_term1|go_id2#go_term2|go_id3#go_term3|...
Pathways (EMD Millipore)
emd millipore_id1#emd millipore_pathway1|emd millipore_id2#emd millipore_pathway2|emd millipore_id3#emd millipore_pathway3|...
Pathways (Sigma-Aldrich)
sigma_summary_id||sigma_id1#sigma_pathway1|sigma_id2#sigma_pathway2|sigma_id3#sigma_pathway3|...
Pathways (CST)
cst_id1#cst_pathway1|cst_id2#cst_pathway2|cst_id3#cst_pathway3|...
Pathways (KEGG)
kegg_id1#kegg_pathway1|kegg_id2#kegg_pathway2|kegg_id3#kegg_pathway3|...
Tocris Compounds
compound1#action#CAS number|compound2#action#CAS number|compound3#action#CAS number|...
HMDB Compounds
compound1#synonyms#CAS number#pubmed_ids|compound2#synonyms#CAS number#pubmed_ids|compound3#synonyms#CAS number#pubmed_ids|...
DrugBank Compounds
compound1#synonyms#CAS number#type#actions#pubmed_ids|compound2#synonyms#CAS number#type#actions#pubmed_ids|compound3#synonyms#CAS number#type#actions#pubmed_ids|...
Novoseek Compounds
compound1|compound2|compound3|...
PharmGKB Compounds
compound1#relations#pubmed_ids|compound2#relations#pubmed_ids|compound3#relations#pubmed_ids|...
TarThera Compounds
compound1|compound2|compound3|...
Transcripts (Refseq)
transcript1|transcript2|transcript3|...
Transcripts (Unigene)
ug_cluster1#description|ug_cluster2#description|ug_cluster3#description...
Expression in Human tissues
probe-set_id1#binary_pattern1#sensitivity1#specificity1|probe-set_id2#binary_pattern2#sensitivity2#specificity2|probe-set_id3#binary_pattern3#sensitivity3#specificity3...
Orthologs
source:organism1#gene1#percent protein similarity#percent nucleotide similarity|organism2#gene2#percent protein similarity#percent nucleotide similarity|organism3#gene3#percent protein similarity#percent nucleotide similarity|...
The organisms are depicted by their two or three letter acronyms as follows:
| Acronym | Scientific name | Common name |
|---|---|---|
| Aga | Anopheles gambiae | African malaria mosquito |
| At | Arabidopsis thaliana | Thale cress |
| Bt | Bos taurus | Cow |
| Cel | Caenorhabditis elegans | Worm |
| Cfa | Canis familiaris | Dog |
| Cin | Ciona intestinalis | Sea squirt |
| Cre | Chlamydomonas reinhardtii | Green algae |
| Ddi | Dictyostelium discoideum | Amoeba |
| Dm | Drosophila melanogaster | Fruit fly |
| Dr | Danio rerio | Zebrafish |
| Eg | Ashbya gossypii | A. gosspyii yeast |
| Gga | Gallus gallus | Chicken |
| Gma | Glycine max | Soybean |
| Hv | Hordeum vulgare | Barley |
| Kl | Kluyveromyces lactis | K. lactis yeast |
| Les | Lycopersicon esculentum | Tomato |
| Mgr | Magnaporthe grisea | Rice blast fungus |
| Mm | Mus musculus | Mouse |
| Mtr | Medicago truncatula | Medicago trunc |
| Ncr | Neurospora crassa | Bread mold |
| Omy | Oncorhynchus mykiss | Rainbow trout |
| Os | Oryza sativa | Rice |
| Pf | Plasmodium falciparum | Malaria parasite |
| Pt | Pan troglodytes | Chimpanzee |
| Pta | Pinus taeda | Loblolly pine |
| Rn | Rattus norvegicus | Rat |
| Sbi | Sorghum bicolor | Sorghum |
| Sc | Saccharomyces cerevisiae | Baker's yeast |
| Sma | Schistosoma mansoni | Schistosome parasite |
| Sof | Saccharum officinarum | Sugarcane |
| Sp | Schizosaccharomyces pombe | Fission yeast |
| Ssc | Sus scrofa | Pig |
| Str | Xenopus tropicalis | Tropical clawed frog |
| Ta | Triticum aestivum | Wheat |
| Tgo | Toxoplasma gondii | Toxoplasmosis |
| Vva | Vitis vinifera | Alicante grape |
| Xl | Xenopus laevis | African clawed frog |
| Zm | Zea mays | Corn |
Homologene Paralogs
gene1|gene2|gene3|...
Ensembl Paralogs
gene1|gene2|gene3|...
Genomic Variants (NCBI)
number of snps: ncbi_id1#location type#minor allele frequency#sample size#populations studied#validation#position#nucleotide change#amino acid change#sequence#number of sources|ncbi_id2#location type#minor allele frequency#sample size#populations studied#validation#position#nucleotide change#amino acid change#sequence#number of sources...
OMIM Disorders
omim_id#disorder_id1|disorder_id2|disorder_id3|...
UniProtKB Disorders
source:uniprotkb_id1#disorder & disorder..|uniprotkb_id2#disorder & disorder..|uniprotkb_id3#disorder & disorder..|...
Novoseek Disorders
disorder1|disorder2|disorder3|...
PharmGKB Disorders
disorder1#relations#pubmed_ids|disorder2#relations#pubmed_ids|disorder3#relations#pubmed_ids|...
TarThera Disorders
disorder1|disorder2|disorder3|...
Publications
pubmed_id1|pubmed_id2|pubmed_id3|...