[DEPRECATED] KnetMiner Release Information

Arabidopsis Knowledge Network

Selected datasets are downloaded using a shell script [link]. The datasets are transferred into individual networks and integrated into an Arabidopsis knowledge network (AraKNET) using Ondex workflows [links]. A break down of information types in AraKNET and links to the raw data is listed below.

Gene-Protein [Ensembl]

In total 32k Arabidopsis genes (including protein-coding and non-coding RNAs) and 35k proteins including alternative splice variants.

• GFF3
• [FASTA] (ftp://ftp.ensemblgenomes.org/pub/current/plants/fasta/arabidopsis_thaliana/pep/Arabidopsis_thaliana.TAIR10.pep.all.fa.gz)

Gene-SNP-Phenotype [Ensembl]

• Arabidopsis GWAS data for 107 phenotypes. Phenotypes are grouped into the four categories flowering, developmental, defense and ionomics. For more information see [Atwell et al, 2010, Nature] (http://www.nature.com/nature/journal/v465/n7298/abs/nature08800.html) and [supplementary information] (http://www.nature.com/nature/journal/v465/n7298/extref/nature08800-s1.pdf).
• Data was downloaded from [Ensembl BioMart] (http://plants.ensembl.org/biomart/martview?VIRTUALSCHEMANAME=plants_mart&ATTRIBUTES=athaliana_eg_snp.default.snp.refsnp_id|athaliana_eg_snp.default.snp.associated_variant_risk_allele|athaliana_eg_snp.default.snp.distance_to_transcript|athaliana_eg_snp.default.snp.chr_name|athaliana_eg_snp.default.snp.chrom_start|athaliana_eg_snp.default.snp.ensembl_gene_stable_id|athaliana_eg_snp.default.snp.consequence_type_tv|athaliana_eg_snp.default.snp.phenotype_name|athaliana_eg_snp.default.snp.phenotype_description|athaliana_eg_snp.default.snp.p_value&FILTERS=athaliana_eg_snp.default.filters.phenotype_significance."1"|athaliana_eg_snp.default.filters.distance_to_transcript."1000"&VISIBLEPANEL=resultspanel )
• SNP-Phenotype relations (122,919 relations) of significant SNPs (as defined by Ensembl, p-value<0.05?) linked to 107 phenotypes; on average 1,150 SNPs per phenotype.
• SNP-Gene relations are based on genes in close proximity to SNPs <1000bp (96,047 relations)
• #SNP=66,816 | #Gene=27,502 | #Phenotype=107
• To see it live, go to KnetMiner and search for dormancy, then switch to Map View.

Gene-GO [GOA]

• Include all evidence types
• [GAF 2.0] (http://www.geneontology.org/gene-associations/gene_association.tair.gz)
• Ondex GAF parser requires additional mapping file of feature type -> Ondex Concept Class

Gene-Gene Interactions [BioGRID]

• [TAB] (http://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-3.4.144/BIOGRID-ORGANISM-3.4.144.tab2.zip)
• Version 3.4.144
• Concepts: 9538 [Gene] | 2326 [Publication]
• Relations: 299 [genetic] | 37756 [physical] | 20044 [pub_in]

Gene-Phenotype [TAIR]

• [TAB] (ftp://ftp.arabidopsis.org/home/tair/User_Requests/Locus_Published_20130305.txt)

Publications [PubMed]

• [XML] (http://www.ncbi.nlm.nih.gov/pubmed/?term=arabidopsis+thaliana)
• 57,600 PubMed abstracts
• filter publications that are unconnected, i.e. not linked via citation or text-mining

Gene-Publication [GOA, TAIR]

• [GAF 2.0] (http://www.geneontology.org/gene-associations/gene_association.tair.gz)
• [TAB] (ftp://ftp.arabidopsis.org/home/tair/User_Requests/Locus_Published_20140331.txt.gz)

Protein-Publication [UniProtKB, TAIR]

• [At proteome XML] (http://www.uniprot.org/uniprot/?query=proteome:UP000006548&compress=yes&format=xml)
• [TAB] (ftp://ftp.arabidopsis.org/home/tair/User_Requests/Locus_Published_20140331.txt.gz)
• relations (pub_in): 65,780
• concepts (Publication): 15,892

Protein-Pathway [AraCyc]

• AraCyc Release 14
• biopax-level2.owl
• Translation.tab

Gene-TO [Text Mining]

• Created 27k Gene-TO sentence based co-occurrences in PubMed abstracts

Sequence alignments to other Plants

• Protein@Arabidopsis-Protein@Plants::UniProtKB-SP [Smith-Waterman]
  • Concepts: 26663 [Protein]
  • Relations: 100947 [h_s_s]
• Protein-GO [UniProtKB]
• Protein-Publication [UniProtKB]

Orthologs in Yeast

• Protein@Arabidopsis-Protein@Yeast::UniProtKB-SP [Inparanoid]
• Protein-GO [UniProtKB]
• Protein-Publication [UniProtKB]
• Protein-Protein Interaction [BioGRID]
• Concepts: 6366 [Protein] | 13725 [Publication]
• Relations: 462411 [genetic] | 97205 [physical] | 155615 [pub_in]

Information types contained in Arabidopsis KNET

Concept Class	Concept Count
Pathway	610
Enzyme	8,666
Publication	70,720
Reaction	3,193
Protein	118,803
Compounds	3,000
Phenotype	6,489
MolFunc	10,542
Gene	31,484
SNP	66,816
BioProc	29,400
CelComp	4,048
Trait (GWAS)	108
TO	1,384
Transport	95
EC	2,254
Protcmplx	193
Total Concepts	368,434