Description of Participating Systems
Below is a list of the systems that are participating in the upcoming BioCreative IV Interactive task. Please note that the systems will be ready for testing by mid August, therefore, some websites may not be yet ready with all functionalities, or may present an overview of the system. Also note that the information in the table is limited to that pertaining to the task proposed for the interactive activity.
Additional documentation on the systems and tasks is found in download section at the end of this page.
To participate in a user study involving one or more of these systems, please click here.
| System | Description | Entity Recognition | Normalization | Categorization | Information Extraction | Text | Browser | Target User |
|---|---|---|---|---|---|---|---|---|
| Argo | Annotation of metabolic process-related named entities, namely chemical entities and genes or gene products. | gene/protein, chemical | UniProtKB (gene/protein), ChEBI (chemicals), CTD (action words) | metabolic process-related action words | Abstract | Firefox, Chrome, Safari | Metabolic pathway Databases, small compound databases | |
| BioQRator | Validate retrieved articles based on relevance on protein-protein interaction information | gene/protein involved in PPI | PPI | Abstract | Firefox, Chrome, Safari, Explorer | PPI Databases | ||
| Cell Finder | Annotation of gene, expression relation and cell type in text snippets from a set of articles | gene, cell type | PubMed search using MedLine Ranker | expression-related action words | Text snippets | Firefox, Chrome, Safari, Explorer | Databases that annotate gene expression | |
| EGAS | Identification and extraction of PPI events desribed over PubMed abstracts related to neuropatological disorders | protein | PPI | PPI-related action words | Full length | Firefox, Chrome, Safari | Databases that capture relation among proteins | |
| MarkerRIF | Triage on disease-biomarker, and extraction of these entities with normalization | gene/protein(biomarkers), disease | EntrezGene, MeSH | disease-biomarker | disease-biomarker | Abstract | Firefox, Chrome | Databases that annotate biomarker/disease information, Pharma companies |
| Ontogene | Detection of Gene/Chemical/Diseases and their interactions | gene/chemical/diseases | CTD identifiers | Gene/Chemical/Diseases interactions | Abstract | Firefox, Chrome, Safari | Pharma companies, disease/gene-centric databases | |
| RLIMS-P | Annotation of kinase, substrate and site with normalization information. | protein | UniProtKB | phosphorylation | phosphorylation-related action words | Abstract | Firefox, Chrome, Safari | Phosphorylation-related databases, PPI databases |
| SciKnowMine | Triage based on pre-trained categories of interest | system is trained on categories of interest based on previously classified documents | Full length (PDF) | Databases that need article classification in different annotation categories (phenotype, functional annotation, etc). Development of an extensible platform for other annotations and document management. | ||||
| Tagtog | Annotation of gene names within full-text documents especially machine-predicted documents | gene | Full length | Firefox, Chrome | Model Organism database |
