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[DEPRECATED] KnetMiner Release Information

Ajit Singh edited this page Sep 23, 2019 · 1 revision

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.

Gene-SNP-Phenotype [Ensembl]

Gene-GO [GOA]

Gene-Gene Interactions [BioGRID]

Gene-Phenotype [TAIR]

Publications [PubMed]

Gene-Publication [GOA, TAIR]

Protein-Publication [UniProtKB, TAIR]

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
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