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EBIMed specifications


Unique identifier OMICS_01180
Name EBIMed
Interface Web user interface
Restrictions to use None
Output data The results are shown in a table that displays all the associations and links to the sentences that support them and to the original abstracts.
Computer skills Basic
Stability Stable
Maintained No


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Publication for EBIMed

EBIMed citations


Triage by ranking to support the curation of protein interactions

PMCID: 5502361
DOI: 10.1093/database/bax040

[…] tter triage, the search engines we explore in this report will also be more specialized and address more specific curation needs. Although they may not perform better than existing ones (e.g. PubMed, EBIMed, EAGLi…) as general-purpose search tools, we expect they will be optimal to rank the literature given a particular annotation task. In previous works, we presented successful examples of custom […]


PubstractHelper: A Web based Text Mining Tool for Marking Sentences in Abstracts from PubMed Using Multiple User Defined Keywords

PMCID: 4261117
PMID: 25512689
DOI: 10.6026/97320630010708

[…] urring in the same sentence. While many previous studies have developed websites and databases to help researchers in this context, these resources have a number of limitations, as outlined below.EBIMed can be used to find genes and keywords related to proteins, Gene Ontology (GO) annotations, drugs and cancers that co-occur in the same sentences []. The BSQA shows abstracts which contain k […]


Proteomics for systems toxicology

Comput Struct Biotechnol J
PMCID: 4212285
PMID: 25379146
DOI: 10.1016/j.csbj.2014.08.004

[…] and concisely collect up-to-date information on a given protein. However, it does not allow querying specific concepts and biological contexts. This is supported by specific text-mining tools such as EBIMed , SciMiner , and PolySearch . EBIMed and SciMiner accept free literature queries as the input and automatically identify and associate the proteins, functions, and drugs reported in the identif […]


Large Scale Structure of a Network of Co Occurring MeSH Terms: Statistical Analysis of Macroscopic Properties

PLoS One
PMCID: 4090190
PMID: 25006672
DOI: 10.1371/journal.pone.0102188

[…] relevant and interpretable knowledge. A plethora of applications have been developed exploiting co-occurrence for mining interesting patterns in biomedical resources (e.g., BITOLA , iHOP , AliBaba , EBIMed , FACTA , PLAN2L , STRING , LAITOR ).Analyzing big relational datasets requires innovative methodological approaches beyond the basic exploratory mining. Recent years have seen an increasing in […]


Assisted Knowledge Discovery for the Maintenance of Clinical Guidelines

PLoS One
PMCID: 3639894
PMID: 23646153
DOI: 10.1371/journal.pone.0062874

[…] nteracting with information retrieval engines. The past years have seen the development of a wealth of search engines and text mining instruments to navigate the biomedical literature (e.g. GoPubMed, EBIMed, etc.). However, these information retrieval systems often generate high volumes of information at the expense of specificity and sensitivity to the query at hand: they provide the users with a […]


Automated Patent Categorization and Guided Patent Search using IPC as Inspired by MeSH and PubMed

J Biomed Semantics
PMCID: 3632996
PMID: 23734562
DOI: 10.1186/2041-1480-4-S1-S3

[…] terms from existing taxonomies or ontologies - either by using existing manual annotations or by automatically assigning relevant terms. Systems based on this principle include GoPubMed [] as well as EBIMed [] and its sister application Whatizit []. All these systems are mainly or exclusively intended for use with Medline/PubMed documents; there is no comparable system for patents. Consequently, i […]


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EBIMed institution(s)
European Bioinformatics Institute (EBI), Wellcome Trust Genome CampusHinxton, Cambridge, UK

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