e-journal

The KnownLeaf literature curation system captures knowledge aboutArabidopsis leaf growth and development and facilitates integrateddata mining

---

The information that connects genotypes and phenotypes is essentially embedded in research articleswritten in natural language. To facilitate access to this knowledge, we constructed a framework for thecuration of the scientific literature studying the molecular mechanisms that control leaf growth anddevelopment in Arabidopsis thaliana (Arabidopsis). Standard structured statements, called relations, weredesigned to capture diverse data types, including phenotypes and gene expression linked to genotypedescription, growth conditions, genetic and molecular interactions, and details about molecular entities.Relations were then annotated from the literature, defining the relevant terms according to standardbiomedical ontologies. This curation process was supported by a dedicated graphical user interface, calledLeaf Knowtator. A total of 283 primary research articles were curated by a community of annotators,yielding 9947 relations monitored for consistency and over 12,500 references to Arabidopsis genes. Thisinformation was converted into a relational database (KnownLeaf) and merged with other public Ara-bidopsis resources relative to transcriptional networks, protein–protein interaction, gene co-expression,and additional molecular annotations. Within KnownLeaf, leaf phenotype data can be searched togetherwith molecular data originating either from this curation initiative or from external public resources.Finally, we built a network (LeafNet) with a portion of the KnownLeaf database content to graphicallyrepresent the leaf phenotype relations in a molecular context, offering an intuitive starting point forknowledge mining. Literature curation efforts such as ours provide high quality structured informationaccessible to computational analysis, and thereby to a wide range of applications.DATA: The presented work was performed in the framework of the AGRON-OMICS project (ArabidopsisGRO wth Network integrating OMICS technologies) supported by European Commission 6th FrameworkProgramme project (Grant number LSHG-CT-2006-037704). This is a data integration and data sharingportal collecting all the all the major results from the consortium. All data presented in our paper isavailable here. https://agronomics.ethz.ch/.

Keywords:ArabidopsisLeaf growthLiterature curationData integrationa

---

Ketersediaan

Tidak ada salinan data

Informasi Detail

Judul Seri

Current Plant Biology

No. Panggil

-

Penerbit

: Elsevier., 2015

Deskripsi Fisik

Current Plant Biology 2 (2015) 1–11

Bahasa

English

ISBN/ISSN

-

Klasifikasi

-

Tipe Isi

-

Tipe Media

-

Tipe Pembawa

-

Edisi

-

Subjek

KIMIA

Info Detail Spesifik

-

Pernyataan Tanggungjawab

Wati/Agus

Versi lain/terkait

Lampiran Berkas

Komentar

---

Anda harus masuk sebelum memberikan komentar