Indexed Genome Annotation Databases

The focus of LAILAPS in the EU transPlant consortium is towards an explorative information retrieval in plant genomes. The transPlant LAILAPS server index major genome annotation hubs for plant genomes. In summary, the index comprise more than 50,000,000 records from 13 genome annotation targets:

Ontologies

  • Gramene Taxonomy Ontology
    Primarily derived from NCBI Taxonomy, this taxonomy ontology focuses on the Poaceae (Gramineae) family of plant taxonomy only.
  • NCBI Taxonomy
    The Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases.
  • Plant Ontology (PO) Controlled vocabulary (ontology) that describes plant anatomy and morphology and stages of development for all plants.
  • Gene Ontology Consortium
    The Gene Ontology Consortium project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases.

Protein Sequence Databases

  • Pfam
    A large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)
  • UniProtKB/Swiss-Prot
    The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. The Swiss-Prot section contain manually-annotated records.
  • UniProtKB/TrEMBL
    • UniProtKB/TrEMBL contains high quality computationally analyzed records that are enriched with automatic annotation and classification.
  • RCSB PDB
    The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies.
  • InterPro
    InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. We combine protein signatures from a number of member databases into a single searchable resource, capitalising on their individual strengths to produce a powerful integrated database and diagnostic tool.

Plant Diversity Resources

  • Taxonomic Allium Reference Collection
    Scientific name, source of material, availability, taxonomic affiliation, and (as far as available) graphical schemes of chromosomal shape as well as up to 5 voucher photographs of the definitely determined accessions are shown.
  • Garlic Shallot Core Collection (GSCC)
    The Garlic and Shallot Collection hosted at the IPK comprises germplasm of 540 accessions in total. The web application of the Garlic and Shallot Core Collection is the presentation of passport and characterization and evaluation data.
  • GBIS-I Genebank Information System of the IPK Gatersleben
    GBIS/I allows to retrieve information from the German federal ex situ collection.

Biomedical Literature Databases

  • PubMed
    PubMed comprises more than 24 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.