Angiogenesis Extraction

Angiogenesis Extraction Demo

The demonstration systems will automatically highlight terms and events describing angiogenesis bioprocess, as well as biological entities such as gene, gene product, tissue and cell. A Conditional Ramdom Fields (CRF) model is employed for tagging the named entities, while 3 different methods can be chosen for the extraction of angiogenesis events:

CRF: also uses a CRF model, trained on the angiogenesis corpus.
Keyphrase: constructs angiogenesis events using predicate argument relations generated by the ENJU syntactic parser and domain-specific key words/phrases, which were automatically extracted by comparing domain-specific and general corpora. For the moment this method is relatively slow as it calls the syntactic parser to analyse the text at run time.
Dictionary: performs longest-match string searching using a semi-automatically compiled dictionary of phrases describing angiogenesis.

Paste a piece of text into the box below and press one of the 3 buttons. Or select:

Sample text:

MEK5/ERK5 signaling modulates endothelial cell migration and focal contact turnover.
The formation of new blood vessels from pre-existing ones requires highly coordinated restructuring of endothelial cells (EC) and the surrounding extracellular matrix. Directed EC migration is a central step in this process and depends on cellular signaling cascades that initiate and control the structural rearrangements. On the basis of earlier findings that ERK5 deficiency in mouse EC results in massive defects in vessel architecture, we focused on the impact of the MEK5/ERK5 signaling pathway on EC migration. Using a retroviral gene transfer approach, we found that constitutive activation of MEK5/ERK5 signaling strongly inhibits EC migration and results in massive morphological changes. The area covered by spread EC was dramatically enlarged, accompanied by an increase in focal contacts and altered organization of actin filaments. Consequently, cells were more rigid and show reduced motility. This phenotype was most likely based on decreased focal contact turnover caused by reduced expression of p130Cas, a key player in directed cell migration. We demonstrate for the first time that ERK5 signaling not only is involved in EC survival and stress response but also controls migration and morphology of EC.

* This is a demo version and please limit your input to 4096 characters.

Xinglong Wang | National Centre for Text Mining | School of Computer Science | University of Manchester