SEARCHING BIOTECHNOLOGY INFORMATION IN THE 2010s: Section II (Databases & Search Strategies)

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SEARCHING BIOTECHNOLOGY INFORMATION IN THE 2010s:

Section II (Databases & Search Strategies)

Luca Falciola, IP Manager, Promethera Biosciences

Sardegna Ricerche-Univ. Cagliari (Sep. 15^th 2014)

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Databases & Biotechnology : A foreword

 Covering even a limited number of databases is already pretty impossible and a selection is required according to a few criteria

 Free access (at most, requiring the registration at a website using a user/password and an e-mail to get full access to services ; at this scoep better using a separate, specific free e-mail on the Internet to be used only at this scopes and for receiving Table of Contents, updates etc.)

 Overall positive reputation , importance , and good

« search experience » even for occasional user

 This selection can be easily expanded for specific objectives by

 Searching the structured repertory in Nucl. Acid Res . website and the yearly update

 Combining search topic in Google and/or Pubmed

 Exploring he NCBI and EBI websites

Sardegna Ricerche L. Falciola 15/09/2014

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1 Scientific Literature

- Pubmed HighWire - Publishers’ website 2 Patent Literature

3 Chemical Structure & Biological Sequences 4 Metabases

DATABASES FOR BIOTECHNOLOGY INFORMATION

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 The databases of scientific literature are several, mostly thematic, and Pubmed has a major role in life sciences

 More than 1,2 entries for year 2013, for a total of more than 25 millions

 Considered by many as the most complete database

 This leadership should not forget other resources that, at different levels, may be competitive for identifying relevant literature

 Commercial ones (EMBASE, SCISEARCH,SCI VERSE, BIOSIS, etc.)

 Databases covering a large panel of publishers for promoting the purchase of articles that provide full-text search features or other advances search / push services

 The full-text Vs indexing/completeness comparison is actually a main topic

Scientific Literature:

Introduction

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 Pubmed offers almost everything you need with exception of full-text search

 A well organized help page including links to Youtube and other tutorials

 Access to the large panel of services of NCBI as summarized in this guide and this NAR paper

 Sign-in page for accessing a even larger panel of features

 Guides to other literature databases , NCBI digital library, and the MeSH system

Pubmed:

Introduction

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6 Sardegna Ricerche L. Falciola 15/09/2014

 Both features are un the same page that can be maintained or even saved

Pubmed:

Advanced Search and Search History

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 A large number of fields is available for text or numeric searches

Pubmed:

Field Search

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Pubmed:

MeSH Examples (antibodies)

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 Some Pubmed tutorial are too complex and some university provide simplified versions like for MeSH and insisting in

 pursuing a sequential structured approach to identify the more relevant MeSH terms

 Not forgetting that MeSH are not always present and are relevant for extract a more relevant subset of references to explore with a series of related criteria

Pubmed:

MeSH tutorial

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 A large number of operators /symbols expand the possibilities well beyond AND OR NOT (and truncation, double quotes are essential for pursuing precise but not too extensive searches)

 The search can be also improved by the large selection of filters in left sidebar

Pubmed:

Search Operators

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 An important issue is that Pubmed is intended to provide publications as soon to users, explaining some heterogeneity in indexing and access to articles

Pubmed:

Heterogeneity

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 Substitute “” with a – between two words in a phrase

 The use of truncation shows how many spelling errors are present in the database that may make you miss some relevant hits

 Sedn Pubmed reference by e-mail just by indicating the PMID after http://www.ncbi.nlm.nih.gov/pubmed/

eg http://www.ncbi.nlm.nih.gov/pubmed/25031662,25000062

 The « Related » references can be saved in the search history and combined with keywords to search within them

 Search History is limited in time and length (better not exceeding 50-80 entries)

Pubmed:

Some tricks

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 Large literature life science database hosted by Stanford Univ. aggregating journals from many major publishers but also books and conference

abstracts, also as full text and with some useful filters

Highwire Press:

Overview

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Highwire:

Help Page

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Highwire:

Search Results & History

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Highwire:

Services

 Preview of keywords in the context, alerting for new articles including a given citation or keywords, alternative viewing features, links to supplementary/

free documents and management of ToC are well implemented

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 All main publishers with a large panel of journals have nice feature to keep track of new articles or searching heir publications

 Nature, Science, Wiley, Springer

 Scienedirect of Elsevier is particularly rich of functions and has a broad coverage (even of journals not indexed in Pubmed

Publishers’ Website:

Introduction

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Publishers’ Website:

Other Examples

 Wiley

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1 Scientific Literature 2 Patent Literature

- Lens - Espacenet - Patentscope 3 Chemical Structure & Biological Sequences

4 Metabases

DATABASES FOR BIOTECHNOLOGY INFORMATION

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Patent Literature:

Introduction

 Patent information that may be relevant for a biotech search is available in a variety of formats:

 Text-based

 Biological sequences

 Chemical structures

 Regular review of patent publications can be performed by using appropriately three types of tools :

 Multi-Patent offices websites (Patentscope, Espacenet, Lens)

 Patent office-specific tools (at USPTO, EPO, Australian, Indian, etc.) but in general poorly implemented outside basic number or proceedings

 Access for sequence- or structure-based searches (Lens, EBI)

 Each approach and tool has own strengths/weakness:

 Need to compare/double-check

 Access to PDF and identification of keyword context

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Patent Literature:

Overview

 Main strengths :

 Patentscope and Lens: full text/stemmed/nested searches, large number of criteria, login for saving search strategies, graphical/automated grouping of results

 Patentscope and Espacenet: machine-based translation

 Lens: somehow easier to use for both searching and getting/sending links to PDF files, nice support section, possible to search only granted patents, nice sorting/filtering functions, claims and abstract on the same page

 Espacenet: Cooperative Patent Classification & citing/cited documents features for(non-) EP appl. , link to EPO register, links to (often) reliable patent family & Inpadoc/status information

 Main weaknesses:

 Patentscope: unstability in case of long search session, IPC only, no clear patent family information

 Lens: format inconsistency for code/number fields, coverage and patent family definition, with functions appearing and disappearing (now providing IPC and USPC)

 Espacenet: somehow old-style for both searching documents and getting PDF files

 In general:

 No visibility on actual coverage for all collections

 Limited means to identify keyword context

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Lens :

Search window

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Lens:

Search Window

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Lens:

Search Window

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Lens:

Filtering Features

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Lens:

Help Page

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Espacenet:

Search Window and Criteria

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Espacenet:

Patent Kind Codes & Help

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Espacenet:

CPC Classification

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Espacenet:

Results & Record View

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Patentscope:

Search Window & Results

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Patentscope:

Record & Records Analysis

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1 Scientific Literature 2 Patent Literature

3 Chemical Structure & Biological Sequences

-Uniprot - EBI-Fasta - ChEMBL/Pubchem 4 Metabases

DATABASES FOR BIOTECHNOLOGY INFORMATION

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Uniprot:

Overview & Search Criteria

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Uniprot:

Overview & Search Criteria

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Uniprot:

HBB in Genecards Vs Uniprot

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EBI-Fasta:

Search Window

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EBI-Fasta:

Overview of Results

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EBI-Fasta:

Patent Sequence Record

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ChEMBL:

Introduction

 Medicinal chemistry data/products is now more accessible also to non-

specialist through portals such as EBI/ChEMBL, PubChem, or Drugbank portals that aggregate and make them searchable through different criteria, across biological/medical/patent information together with chemical information from proprietary repositories) for creating Molecular Clouds

(Ertl and Rohde, J Cheminf 2012)

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ChEMBL:

Features

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ChEMBL:

Search & Browse Features

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ChEMBL:

Targets, Ligands & Drug Approvals

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1 Scientific Literature 2 Patent Literature

3 Chemical Structure & Biological Sequences 4 Metabases

- Google - Google Scholar - Drugbank

DATABASES FOR BIOTECHNOLOGY INFORMATION

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Google:

Advanced Search & GoogleGuide

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 This site claims having broad coverage of both scientific and patent literature but it is actually unclear the coverage:

 beyond US patent documents and by which date (they index papers and not journals

 of which publishers

 The system has some additional useful features compared to “pure“ Google

 Separate advanced search features

 Management of alerts through own Gmail account

 Import features for reference management systems (but not always precise)

 Selection of publication date instead of appearance on the web (but again not always precise)

 Clear link to PDF on the left side of the window

 Citation list (that can be searched separately) and “related articles” features

 Metrics / search by journal

 Focused help page with advis on how getting your paper indexed

Google Scholar:

Introduction

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Google Scholar:

Advanced Search Features

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Google Scholar:

Settings and Metrics Features

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 Google Scholar provides means for overcoming only some limitations of

“pure” Google

 Lack of visibility about publication/journal coverage

 Unstructured search features within documents

 Lack of indexing

 It is an interesting tool for exploratory searches or completing searches made in “traditional” databases

 Exploiting full-text and advanced search features in a more structured environment

 Linking articles to combinations of specific technical details, cross-references, authors

 Obtaining additional search criteria to be used elsewhere

Google Scholar:

Final Comments

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DrugBank:

Introduction

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DrugBank:

Results

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DrugBank:

Records

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