[DEPRECATED] KnetMiner Release Information - Rothamsted/knetminer GitHub Wiki
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]
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 |