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Ranking search result software tools | Information retrieval

Notable tools for result ranking. Typically, they use a combination of classifiers, such as support vector machines (SVMs) or weight schemes, complemented by artificial intelligence algorithms to rank documents based on MeSH® terms, author names…
Alkemio
Web

Alkemio

Ranks all annotated chemicals (including drugs) in the literature for any…

Ranks all annotated chemicals (including drugs) in the literature for any biomedical topics. The SOAP web service allows the programmatic usage of Alkemio (e.g. for batch queries) from common…

Omicseq
Web

Omicseq

Facilitates the easy interrogation of omics datasets holistically to improve…

Facilitates the easy interrogation of omics datasets holistically to improve ‘findability’ of relevant data. Omicseq uses an algorithm for ranking omics datasets that fully uses the numerical…

RefMED
Web

RefMED

A multi-level relevance feedback system for PubMed. RefMed supports both ad-hoc…

A multi-level relevance feedback system for PubMed. RefMed supports both ad-hoc keyword queries and a multi-level relevance feedback in real time on PubMed. It effectively learns an accurate…

GeneView
Web

GeneView

A semantic search engine for biomedical knowledge. GeneView is built upon a…

A semantic search engine for biomedical knowledge. GeneView is built upon a comprehensively annotated version of PubMed abstracts and openly available PubMed Central full texts. This semi-structured…

Génie
Web

Génie

Prioritizes the whole gene set of hundreds of species for any biomedical topic,…

Prioritizes the whole gene set of hundreds of species for any biomedical topic, taking advantage of annotations-linking genes and bibliography. Génie takes a biological topic as input (ideally…

MedlineRanker
Web

MedlineRanker

A flexible ranking of Medline for a topic of interest without expert knowledge.…

A flexible ranking of Medline for a topic of interest without expert knowledge. MedlineRanker can process thousands of abstracts from the Medline database in few seconds, or millions in few minutes.

Seq2Ref
Web

Seq2Ref

Allows detection of proteins homologous and identification of the reference…

Allows detection of proteins homologous and identification of the reference proteins. Seq2Ref is a homology-based web server to identify reference proteins from PubMed, Protein Data Bank (PDB) and…

OrChem
Desktop

OrChem

Adds registration and indexing of chemical structures to support fast…

Adds registration and indexing of chemical structures to support fast substructure and similarity searching. OrChem is an open source chemistry plugin / cartridge for the relational database system…

SOURCE
Dataset

SOURCE

Displays information about genes including functional, structural and…

Displays information about genes including functional, structural and expression data and also about given cDNA clone (also known as an Expressed Sequence Tag or EST) including putative ID, the size…

MiSearch
Web

MiSearch

An adaptive biomedical literature search tool that ranks citations based on a…

An adaptive biomedical literature search tool that ranks citations based on a statistical model for the likelihood that a user will choose to view them. Citation selections are automatically acquired…

miRAFinder
Desktop

miRAFinder

Simplifies tasks during biological investigations. miRAFinder is a Python…

Simplifies tasks during biological investigations. miRAFinder is a Python package that allows to find miRNA names and keywords. This script was developed for the semi-automatic extraction and…

GeneAFinder
Desktop

GeneAFinder

Simplifies tasks during biological investigations. GeneAFinder is a Python…

Simplifies tasks during biological investigations. GeneAFinder is a Python package that allows to find specific information and gene names in the abstract of PubMed. It is possible to find the list…

PubFocus
Web

PubFocus

Performs statistical analysis of the MEDLINE/PubMed search queries enriched…

Performs statistical analysis of the MEDLINE/PubMed search queries enriched with the additional information gathered from journal rank database and forward referencing database. PubFocus's new…

MScanner
Web

MScanner

An implementation of a Bayesian classifier that provides a simple web interface…

An implementation of a Bayesian classifier that provides a simple web interface for submitting a corpus of relevant training examples in the form of PubMed IDs and returning results ranked by…

Caipirini
Web

Caipirini

A service enabling literature search directly based on biological relevance to…

A service enabling literature search directly based on biological relevance to gene sets. Caipirini gives the research community a new way to unlock hidden knowledge from gene sets derived via…

Chrawler
Desktop

Chrawler Chemistry and Crawler

Federates search of chemical structures and reactions across various data…

Federates search of chemical structures and reactions across various data sources in an enterprise environment. Chrawler is an innovative chem-informatics tool and an enterprise search solution for a…

Semantic…
Web

Semantic MEDLINE

A Web application that summarizes MEDLINE citations returned by a PubMed…

A Web application that summarizes MEDLINE citations returned by a PubMed search. Natural language processing is used to extract semantic predications from titles and abstracts. The predications are…

Quertle
Web

Quertle

Allows a semantic search in multiple biomedical databases (PubMed included) and…

Allows a semantic search in multiple biomedical databases (PubMed included) and runs a query via relationships between concepts, so that you retrieve at ease more pertinent results and can navigate…

eTBLAST
Web

eTBLAST

A program designed to identify similar documents within literature databases…

A program designed to identify similar documents within literature databases such as (but not limited to) MEDLINE. These services are freely accessible through the Internet, where users can upload a…

Olelo
Web

Olelo

Enables real-time responses to researchers’ queries. Olelo combines…

Enables real-time responses to researchers’ queries. Olelo combines biomedical literature and terminologies in a fast in-memory database. It permits a fast and intelligent search through the…

Twease
Web

Twease

A web-based tool to search Medline abstracts. Twease indexes each word of…

A web-based tool to search Medline abstracts. Twease indexes each word of Medline and provides features that can transparently expand your search to help find the information you are looking for.

TAPIR
Web
Desktop
Mobile

TAPIR

Provides a DNA search engine. TAPIR can analyse a sequencing data without any…

Provides a DNA search engine. TAPIR can analyse a sequencing data without any reference genome. It is composed of a server with known reference DNA indexed, and a client with raw sequencing reads.…

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