Search Engines
AA Info

Author: Gianpiero Pescarmona
Date: 11/05/2008



Navigating the future of online scientific research

JournalMap: in partnership with Taylor & Francis

Today, we are pleased to announce further developments in the ongoing and successful relationship between Taylor & Francis and JournalMap.



Fulltext Search Engines

Un nuovo motore di ricerca consente di trovare su internet il testo completo di pubblicazioni in campo biomedico, sociale e ingegneristico

Lo scopo del sito è quello di aumentare la visibilità e di facilitare la ricerca di pubblicazioni ad accesso libero sul web. Sono coperti i seguenti campi della conoscenza: scienze della vita e della salute, fisica, ingegneria, scienze sociali ed umane. Ogni documento può essere scaricato gratuitamente e salvato in formato pdf.

Il sito è stato sviluppato da una azienda di innovazione tecnologica francese ( specializzata nella ricerca e nell’analisi di fonti informative in ambito scientifico. Le pubblicazioni indicizzate nel database sono state selezionate a partire da un insieme di 10,000 fonti informative di tipo tecnico-scientifico e biomedico.

Questa iniziativa, nata da un’azienda che opera nel sud-ovest della Francia, rappresenta la prima volta che un progetto di portata globale prende origine da un Paese sud-europeo.

La ricerca in può essere svolta semplicemente scrivendo le parole chiave nella finestra di dialogo. L’uso della lingua inglese consente la restituzione di un numero maggiore di risultati e di migliore qualità. Per rendere più specifica la ricerca è possibile utilizzare un sistema di ricerca avanzato ricorrendo alle regole descritte al seguente link

Mio commento: non molto bello

Scholarly Search Engines

Scirus (ricerca delle parole chiave su Titolo, Abstract, fulltext, sui brevetti e su Internet)
Crossref home
Crossref (ricerca delle parole chiave su Titolo, Abstract, fulltext)
Web of Science
Google Scholar

The Art of Literature Search - Lab Times July 2009

Medical Search Engines

PubMed (ricerca delle parole chiave su Titolo e Abstract delle pubblicazioni scientifiche)

  • The German Approach to PubMed and more ...

EBI:European Bioinformatics Institute the European answer to PubMed.

Pubget Pubget: the search engine for life-science PDFs
GoPubMed server

PubMed, GoPubMed, ReleMed and Novoseek organise search hits according to controlled

  • what
  • who
  • where
  • when


uses powerful natural clustering technology to organise hits according to phrases in the
abstract. The clusters are displayed hierarchically and clicking on any node in the tree
takes you to the abstracts with links to the PubMed sources.


PubMed con visualizzazione grafica


One of the most enjoyable features of Hubmed is the touchgraph: a visual representation
of related articles arranged as a graph.


is a powerful example of what can be achieved when humans and machines work together, using the relationships between words and ideas to produce a focussed reading list

Trip Database - Clinical Search Engine

The TRIP Database is a clinical search tool designed to allow health professionals to rapidly identify the highest quality clinical evidence for clinical practice.

Find Relationships, not Just Keywords


If you search for two or more terms, you will find occurrences of a conceptual relationship, not just the terms scattered within the same document.

Engines with data clustering (Taxonomies?)

Metamotore con sistema di clustering dei risultati della ricerca.

Interessante la sezione BioMetaCluster che interroga in contemporanea il web, PubMed, Highwire, Science Direct (editore Elsevier), Wiley Journals, Royal Society of Chemistry oltre a OMIM , Clinical e altri siti (selezionabili all’interno di un elenco)

ScienceRoll Search Engine



ReleMed è un motore di ricerca che interroga la base di dati MEDLINE. Basta inserire una o alcune parole, e ReleMed ricerca in MEDLINE i risultati migliori per la tua domanda, mettendo in cima all'elenco i risultati più rilevanti.
La differenza rispetto a PubMed è che pur trovando quasi gli stessi articoli, ReleMed li mostra in un ordine differente, con i più rilevanti in testa.

Nuovo motore di ricerca per mat. biomedico - OREFIL



  • Allows to search for genes in many ways
  • Offers semantic search for genes
  • Scans all the literature in PubMed for genes and gene-related functions
  • Shows information about each gene at a glance
  • Brings it all together

Search within Categories


Search in Life Science

  • Protocols
  • Online Tools
  • Powerpoints
  • Databases
  • Software

Proteins Database

Women Health

2009-04-27T20:08:05 - Elena Giglia

Women Health

21st November 2008, London The Global Library of Women's Medicine has
launched online and is freely available to all. Over 650 world experts
provide a definitive resource on the latest therapeutic options in women's
medicine for doctors and women concerned about their health.
The Library is free to view at

The Global Library of Women's Medicine, was launched at a dinner held at
The Royal College of Obstetricians and Gynaecologists in London last night.

It is a unique web library incorporating a vast range of detailed clinical
information across the whole field of women's medicine. It consists of 442
main chapters and 53 supplementary chapters, supported by over 40,000
references, which will be kept permanently up-to-date. The chapters have been written by more than 650 specialists and will reflect some of the very best worldwide opinion.

The Global Library of Women's Medicine is primarily designed for the medical profession, however, most of the information will also be accessible by anyone else who wants to try and understand more about the therapeutic options available to women, this includes a section on Safer Motherhood

In addition, there are innovative features freely available to registered users, that are aimed at medical professionals, including surgical videos, specialist colour atlases of visual medicine, comprehensive guidance to laboratory tests and the significance of
their results,- and even an option to provide doctors with selected patient information handouts.

The Global Library of Women's Medicine will support doctors and other health professionals in their care of women. As an open access resource it is hoped that in addition to providing an expert resource for the medical profession in the Western World, it may also be of real
value to doctors and others in parts of the Developing World where access to current clinical information has always been challenging.

All the expert authors and editors of The Global Library of Women's Medicine have generously made their contributions without any form of financial remuneration - and the British publishers have originated, developed and implemented the site entirely from their own funds - in order
to support this significant global initiative which it is hoped may make some contribution to the ongoing efforts to improve women's healthcare around the world.

Media Contact:
Laura Cox
Frontline Global Marketing Services Ltd
Tel: +44 (0) 1327 359298
pubmed con visualizzazione grafica
ihop: information hyperlinked on proteins

*Tuesday, March 2, 2010 =97PLoS Launches Fast PDF Access
with Pubget, Makin=
Full Text Article Content More Accessible*

Today PLoS released Pubget links across its journal sites.
Now, when users
are browsing thousands of reference citations on PLoS
journals they will be
able to get to the full text article faster than ever before.

Specifically, when readers encounter citations to articles
as recorded by
CrossRef (which are accessed via the =91CrossRef=92 link
in the =91Cited in=
section of any article=92s Metrics tab), a PDF icon will
also appear if it =
freely available via Pubget. Clicking on the icon will
take you directly to
the PDF.

On launching this new functionality, Pete Binfield,
Publisher of PLoS ONE
and the Community Journals said: =93Any service, like
Pubget, that makes it
easier for authors to quickly find the information they
need is a
welcome addition to our articles. We like how Pubget helps
to break down
content walls in science, letting users get instantly to
the article-level
detail that they seek.=94

In this first phase, PLoS is linking to the free PDFs on
Pubget. For those
citations without a freely available PDF you have two
options. The CrossRef
link will take you to the publishers site, where you can
see if you
have access. Or, if you work for any of the 200+
institutions in Pubget=92s
network (for example MIT, and UCSF), you can use the
citation to get the
subscription PDFs right away on If you want to
add your
institution to the Pubget network, just tell your library
=96 Pubget is fre=

2009-04-27T14:27:45 - Elena Giglia

Quertle uses advanced semantic-based searching to find the
most relevant documents. Let Quertle save you from
drowning in your literature search results.



Search within the full article, including Methods. An
initial collection of full-text articles from the 200+
journals from BioMed Central) have been added; more coming

Easier to use, with more hints to help users get the most
out of relationship searching.

The relevant relationships from each article are now
grouped together.

New option for viewing results.

Many new Power Terms, representing entire classes of
entities, have been added. See
for the full list of Power Terms.

Check out the current COASTER contest on the Quertle site!
You could win $50!

for contest rules

Follow "Quertle" on Twitter... watch our progress and keep
updated on new features.

NextBio is the provider of an innovative platform that enables life science researchers to search, discover, and share knowledge locked within public and proprietary data. NextBio's platform seamlessly combines powerful tools with unique correlated content to transform information into knowledge, providing the foundation for new scientific discoveries. NextBio helps organizations increase productivity and dramatically improve collaboration across therapeutic groups and geographic boundaries. NextBio is delivered as a SaaS (Software as a Service) solution resulting in quick deployment and rapid return on investment.

Founded in 2004, NextBio has a rich history of innovation and growth and is recognized as a leader in life sciences knowledge discovery. The company is headquartered in Cupertino, California, employs over 50 people, and serves over a million researchers at the world's top commercial and academic institutions.
Addressing Key Challenges Facing Life Scientists

The NextBio team understands the challenges that are facing the life sciences industry and has developed a specialized set of tools and services to extract knowledge from disparate biological, clinical, and chemical data, regardless of data type and origin. Using NextBio, researchers are empowered to:

* Quickly access relevant, high quality information in seconds vs. weeks
* Search across and examine data, not merely text, across heterogeneous data types
* Upload internal data and correlate it with a pre-existing pool of data in the community
* Discover actionable knowledge without needing an IT consultant or bioinformatician


NextBio provides a robust platform and a comprehensive suite of products. Below is a list of the NextBio products.

NextBio Basic — used by over a million scientists globally to search, discover, and share knowledge extracted from public data repositories, literature, and clinical trials.

2008-08-06T19:55:38 - Gianpiero Pescarmona

New Search Engines based on PubMed

Quertle - - Relationship-driven
Biomedical Search

Quertle is the easiest to use, yet most powerful search
engine for the biomedical literature. Using
cutting-edge, semantic-driven text analytics Quertle
finds conceptual relationships, not just query terms
scattered throughout a document. Quertle's innovative
Power Terms�, representing entire classes of related
concepts such as "diseases", and automatic
identification of key concepts provide the user with
the relevant literature and an intuitive way to
explore it. Try it now at!

Watch a short movie to learn about Quertle.

MORE CONTENT - All of PubMed, full-text articles from
BioMed Central
and PubMed Central, biomedical news, and whitepapers.

GET ANSWERS, NOT JUST LISTS - Using Power Terms and
Quertle's automatic
identification of key concepts, answer questions
such as "What $Proteins regulate apoptosis?".

EXPORT - Save results to your favorite bibliographic
management software
or to a file. The Results pages are also

Quertle is adding link resolving. Contact Quertle
( to
connect your institution's subscriptions directly to
Quertle results.

the Literature, Hot
Search Topics, site updates, and more. Send an email

GET A QUERTLE COASTER - You could win $50 just for
using the site! For
contest rules and to request a coaster go to
Enter "BMC3" in the Promotion Code box and we'll
send you 2 coasters for double the chance to win!

FOLLOW "QUERTLE" ON TWITTER - watch our progress and
keep updated on new



New OA search tool for PubMed
Kevin Davies, Bioalma Launches Novoseek PubMed Search
Tool, Bio-IT World, February 3, 2009. (Thanks to

Bioalma, the Spanish biomedical IT/text-mining
company, has launched a free search tool for the
PubMed literature database called novo|seek, which the
company claims provides intelligent search
functionality to help life scientists guide and refine
their searches of the biomedical literature.

The company calls novo|seek “a dynamic information
extraction system” for searching biomedical records in
repositories, particularly PubMed. Novo|seek indexes
the biomedical literature in PubMed and enables
researchers to find relevant results efficiently by
using external sources of data and contextual term
information. The tool provides familiar chronological
listings of search results, but a sidebar presents a
series of additional related terms based on relevancy,
allowing researchers to drill down and refine
additional queries. ...

Bioalma downloads and indexes 18 million documents in
Medline each day. That information is then put into
the company’s own database using the open-source
Lucene search engine library. ...

While Bioalma believes that novo|seek will help
introduce its other products to a broader audience, it
also hopes to generate revenue by selling online
advertizing through Google ads, targeting companies
selling reagents or equipment. Bioalma has not held
discussions with NCBI about the tool. ...

The first release of novo|seek focuses on PubMed, but
in time Bioalma plans to integrate additional
resources, such as grant information and full-text
Friday, February 27, 2009

Open data from Merck

John Wilbanks, Sage - Open Access Data from Merck, Common
Knowledge, February 27, 2009. Excerpt:

Big news today at the CHI Medicine Tri-Conference.
Merck has pledged to donate a remarkable resource to
the commons - a vast database of highly consistent
data about the biology of disease, as well as software
tools and other resources to use it. The resources
come out of work done at the Rosetta branch of
Merck....In use inside Rosetta/Merck last year alone
it led directly to a ton of publications.

This is all going to happen through the establishment
of a non-profit organization called Sage to serve as
the guardian of the resources. It's not about making a
quick data dump onto the web, however. Sage is going
to take a while during an "incubation period of three
to five which new project data are
generated, critical tools for building and mining
disease models are developed and governing rules for
sharing, accessing, and contributing to the platform
are established."

This is complex content and it's going to take some
ongoing work to expose everything in a usable way. But
the resources are headed for the public domain, and
will be a remarkable capacity builder for those who
currently work without the best tools and data as a
base for their science. Sage means that we are now on
the path to a world in which scientists working on HIV
in Brazilian non-profit research institutes (like my
mother-in-law) will be able to use the same powerful
computational disease biology tools as those inside
Merck. I'm very much looking forward to living in that

I am proud to serve on the founding Board of Directors
for Sage. I hope to play a role in making sure that
the Open Access part of Sage's mission comes to life
in a way that not only keeps the content and resources
available to all, but serves as a key for future
growth and applications. The law isn't the big story
here - the science is - but if we can get the law
right, it can catalyze the emergence of a robust
public domain in disease biology for us all to benefit

This is an incredibly significant step on the road to
open biology - time will tell if it's as earthshaking
as IBM's embrace of GNU/Linux - and I can't wait to
see where it all goes. Congratulations to the team
that built this platform and then had the vision to
take it into the commons.


* Kudos to Merck for this unusually beneficial change
of policy. Kudos too for the good judgment to put
Wilbanks on the Board.
* Less than two weeks ago, GlaxoSmithKline (GSK) also
took a large step toward sharing its knowledge and
intellectual property. We can't say that the pharma
industry is collectively moving toward OA. But it's
showing a pattern of large and small steps toward what
some call pre-competitive sharing. See our past posts
on OA-related activity at BIOS and Cambia, Celera,
Collaborative Drug Discovery, Galapagos, GSK, Lilly,
Merck, Novartis, Pfizer, and Synaptic Leap. The best
analysis of this trend I've read is still Tapscott and
Williams from March 2007.


Subject: Hakia un motore di ricerca semantico per migliorare la qualita`
ricerca in PUBMED

Hakia è un motore di ricerca semantico (basato
su ontologie), a differenza di altri motori di ricerca come Google o
Nel recuperare informazione nell'ambito biomedico Hakia ha incorporato
nel suo motore di ricerca 10 milioni di articoli da PubMed. In effetti,
anche Google Scholar interroga PUBMED; la differenza consiste nel fatto
che Hakia ha un suo algoritmo di ordinamento dei risultati tramite la
tecnologia QDEX (Query Detection and Extraction) che permette un
recupero, in principio, di qualita' migliore dello stesso motore di
La versione Beta e' disponibile su
Maggiori informazioni si trovano sul blog di Hakia:

Fonte: CIBER Newsletter, 19 giugno 2008

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