Output File Format

This page provides information about the format of the output file supplied by the GeneALaCart Batch Queries engine of GeneCards.

General Comments

• 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 is for human genes only, and consists of GeneCards symbols, GeneCards 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 up to 500 genes) or when querying by uploading large files (over 250 genes up to 500 genes).

  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, Entrez Gene, 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) Entrez Gene, OMIM, GeneLoc, Ensembl
  Summaries	EntrezGene, UniProtKB, Tocris	EntrezGene, UniProtKB/Swiss-Prot, Tocris
  Genomic Views	SABiosciences Regulatory transcription factor binding sites, Chromosome, strand, cytogenetic band, genomic location start/end, gene size, Mapped to contig (flag if the information is not genomic), contig	SABiosciences, GeneLoc, NCBI, Ensembl, Entrez Gene, HGNC, HORDE, miRBase
  Proteins	Aliases, UniProtKB ID, UniProtKB Secondary accessions, 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
  Function	UniProtKB ID, UniProtKB function, MGI mutant phenotype, SABiosciences bound target genes, QIAGEN regulating microRNAs	UniProtKB, MGI, SABiosciences, QIAGEN
  Ontologies	GO ID, GO term	GO
  Pathways and Interactions	EMD Millipore ID, EMD Millipore pathway description, R&D Systems pathway description, QIAGEN pathway description, CST(Cell Signaling Technology) ID, CST pathway description, Tocris ID, Tocris pathway description, Thomson Reuters ID, Thomson Reuters pathway description, BioSystems pathway description, Reactome ID, Reactome pathway description, PharmGKB pathway description, KEGG ID, KEGG pathway description	EMD Millipore, R&D Systems, QIAGEN, CST, Tocris, Thomson Reuters, BioSystems, Reactome, PharmGKB, 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
  Transcripts	Refseq transcripts, Unigene cluster, Unigene cluster description, Ensembl transcripts	RefSeq, Unigene, Ensembl
  Orthologs	Organism, gene, percent protein similarity to the human gene, percent nucleotide similarity to the human gene, Entrez Gene ID, GenBank ID, Protein ID	HomoloGene, euGenes, MGI, SGD
  Ensembl pan Orthologs	Organism, gene, percent amino acid similarity to the human gene, orthology type	Ensembl pan taxonomic compara
  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, SABiosciences cancer mutation PCR arrays	NCBI, SABiosciences
  OMIM disorders	OMIM ID, Disorder ID	OMIM
  MalaCards disorders	Disorder description	MalaCards
  UniProtKB disorders	UniProtKB ID, Disorder description	UniProtKB
  Novoseek disorders	Disorder description	Novoseek
  DISEASES disorders	Disorder description	DISEASES
  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

SABiosciences Regulatory transcription factor binding sites(tfbs)

Tfbs1|Tfbs2|Tfbs3|....

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

Contig

For genes that don't have a chromosomal location

UniProtKB Protein details

source:aliases|uniprotkb protein_id1#uniprotkb secondary accessions1#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#uniprotkb secondary accessions2#protein name#size#cofactor..#subunit..#subcellular location..#tissue specificity..#developmental stage..#ptm..#miscellaneous..|
uniprotkb protein_id3#uniprotkb secondary accessions3#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..|...

Function - UniProtKB

source:uniprotkb_id1#function|uniprotkb_id2#function|uniprotkb_id3#function...

Function - MGI mutant phenotype

Allele1: MGI_id1#Phenotypes: |Allele2: MGI_id2#Phenotypes: phenotype_id1#phenotype_name||phenotype_id2#phenotype_name...

Function - SABiosciences bound target genes

gene1|gene2|gene3|...

Function - QIAGEN regulating microRNAs

microRNA_id1|microRNA_id2|microRNA_id3|...

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 (R&D Systems)

r&d systems_pathway1|r&d systems_pathway2|r&d systems_pathway3|...

Pathways (QIAGEN)

qiagen_pathway1|qiagen_pathway2|qiagen_pathway3|...

Pathways (CST)

cst_id1#cst_pathway1|cst_id2#cst_pathway2|cst_id3#cst_pathway3|...

Pathways (Tocris)

tocris_id1#tocris_pathway1|tocris_id2#tocris_pathway2|tocris_id3#tocris_pathway3|...

Pathways (Thomson Reuters)

thomson reuters_id1#thomson reuters_pathway1|thomson reuters_id2#thomson reuters_pathway2|thomson reuters_id3#thomson reuters_pathway3|...

Pathways (BioSystems)

biosystems_pathway1|biosystems_pathway2|biosystems_pathway3|...

Pathways (Reactome)

reactome_id1#reactome_pathway1|reactome_id2#reactome_pathway2|reactome_id3#reactome_pathway3|...

Pathways (PharmGKB)

pharmgkb_pathway1|pharmgkb_pathway2|pharmgkb_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|...

Transcripts (Refseq)

transcript1|transcript2|transcript3|...

Transcripts (Unigene)

ug_cluster1#description|ug_cluster2#description|ug_cluster3#description...

Transcripts (Ensembl)

transcript1|transcript2|transcript3|...

Orthologs

source:organism1#gene1#percent protein similarity#percent nucleotide similarity#entrezgene_id#genbank_id#protein_id|organism2#gene2#percent protein similarity#percent nucleotide similarity#entrezgene_id#genbank_id#protein_id|organism3#gene3#percent protein similarity#percent nucleotide similarity#entrezgene_id#genbank_id#protein_id|...

The organisms are depicted by their two or three letter acronyms as follows:

source:organism1#gene1#percent amino acid similarity#orthology type|organism2#gene2#percent amino acid similarity#orthology type|organism3#gene3#percent amino acid similarity#orthology type|...

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...

Genomic Variants (SABiosciences Cancer Mutation PCR Arrays)

sabiosciences_id1#sabiosciences_cancer_array1|sabiosciences_id2#sabiosciences_cancer_array2|sabiosciences_id3#sabiosciences_cancer_array3...

OMIM Disorders

omim_id#disorder_id1|disorder_id2|disorder_id3|...

MalaCards Disorders

disorder1|disorder2|disorder3|...

UniProtKB Disorders

source:uniprotkb_id1#disorder & disorder..|uniprotkb_id2#disorder & disorder..|uniprotkb_id3#disorder & disorder..|...

Novoseek Disorders

disorder1|disorder2|disorder3|...

DISEASES Disorders

disorder1|disorder2|disorder3|...

Publications

pubmed_id1|pubmed_id2|pubmed_id3|...