Smart Biomedical research through online tool

1. Smart Research through Online Tools
Dr Anwar Siddiqui

2. Topics
Literature Search
Reference Management tools
Where to publish
Managing Research Profiles
Measuring the citation impact of your research
Research Data Management Tools

3. Literature Search

4. Search tools
&
platforms
• Web-Scale Discoverysearch ( Single Window Search @ AML)
• Need to know which resources are indexed in EDS and which are not.
• Search strategy, advancedsearch, refine your search result
• Google Scholar
• Library links on Google Scholar
• Full-text databases
• Examples : ScienceDirect, Springer, Wiley, T&F ….
• Specialized databases(not indexed in Discovery Service)
• Examples : UptoDate, Indiastat,Prowess, PQDT ( Proquest Theses and
Dissertations)…
• General Abstract and Index databases
• Examples : SCOPUS, Web of Science
• Subject Indexes
• SciFinder Scholar, Psychinfo…

5. Wherecan
youfindthe
specifictypes
of literature?
Types of Literature Where can you search
Articles Single Window search, Google Scholar, publisher
platforms, Subject indexes, General A&I
Books Single Window search, Google Scholar, publisher
platforms, Subject indexes, General A&I
Conferenceproceedings Single Window search, Google Scholar, publisher
platforms, Subject indexes, General A&I
ResearchData Google Dataset Search, Harvard Dataverse,Mendeley
Data
Dissertationsor Theses PQDT, NDLTD Globalsearch,
Patents US Patent full-text databases , Google patents ,
CanadianPatentsDatabase, Other internationalpatent
offices, WIPO (World IntellectualProperty
Organization)
Other data & literature Special databasePlatforms, websites etc.

6. Openaccess
resources
• Many of the open-access resources (e-
journals, e-books and conference
proceedings) are included in EBSCO Discovery
service (Single Window Search).
• If your library configured OA in Single
Window Search, you can make use of that.

7. Openaccess
sources-
Books
• Directory of Open Access Books (DOAB)
• Open Access Publishing in European Networks
(OAPEN)
• Open Book Publishers
• SpringerOpen Books
• Taylor & Francis Books Open Access
• Open Humanities Press: Books
• Digital Public Library of America (DPLA)
• Gallica: The French National Library Online
• HathiTrust
• Internet Archive
• LibriVox
• Open Culture: eBooks
• Project Gutenburg

8. Openaccess
sources-
Journals
• BioMed Central (BMC)
• Directory of Open Access Journals (DOAJ)
• Elsevier Open AccessJournals
• Hindawi (Publishing Open AccessResearch Papers
and Journals)
• Open Biology
• Open Humanities Press (OHP): Journals
• Open Library of the Humanities
• Public Library of Science (PLoS)
• Royal Society Open Science
• SpringerOpen
• PubMed
• Taylor & Francis Online: Open journals
• Wiley Open Access

9. Openaccess
sources-
Repositories
• CORE
• Directory of Open Access Repositories
• EBSCO Open Dissertations
• E-Theses Online Service (EThOS)
• Networked Digital Library of Theses and
Dissertations (NDLTD)
• Open Access Theses and Dissertations (OATD)
• ProQuest Dissertations & Theses-open
• Theses Canada
• Thesis Commons
• Shodhganga

10. Reference Management

11. Reference Management tools
• Open access tools
• Mendeley (https://zu.libguides.com/Mendeley)
• Zotero
• Endnote web (Free with Web of Science)
• Other tools (Subscription needed)
• Refworks
• Endnote

12. Where to publish?

13. Where to
publish
Publishing of research findings is crucial to share your
findings with others so that they can benefit from the
new knowledge you have discovered. It also gives your
project findings the opportunity to be critically
evaluated, reproduced and thus gains validity.
If you decide to publish your research in a journal or
present at a conference, you need to find out the
following:
• Is there a peer reviewed process?
• What is the quality of the publication?
• If a journal---do you know the Impact Factor?
• If a journal--how is it perceived within its field?

14. Finding good
journalsto
publish
How to find and evaluate journals.These tools will help you.
• Scimago Journal & Country Rank
• Scopus journal list
• Web of Science Master Journal List
• Elsevier Journal Finder tool
• Wiley Journal Finder
• Springer Journal Suggester
• http://www.sjfinder.com/
• https://www.journalguide.com/
• Journal/Author Name Estimator (JANE)- for Bioscience topics
• Cabell's Whitelist - Subscription needed
• Journal Citation Reports - Clarivate– Subscription needed
• UGC- CARE list (For Indian Scholars)

15. SCImago journal ranking

16. Open access publications
A paper published via an open access (OA) route means that research literature is
free-to-view by anyone in the world via the internet, and to reuse with a attribution
under a Creative Commons licence, or equivalent.
Three types of OA,
• Pure ‘Gold’ OA Publishing - Articles are peer reviewed, selected and formally
published and then made available with no subscription pay-walls.
• Hybrid journals - This is the practice of making articles published in traditional
subscription journals freely available
• ‘Green’ Open Access Archiving - This relates to the practice of archiving a version
of the article somewhere other than the publisher’s website where the final
version of the article is hosted.

17. Open Access – Article publishing charges
• Authors may need to pay Article Publishing
Cost to (APC) to the publisher in most of the
cases.
• Some Universities have institutional
agreement with publishers to pay the APC.
• There are various models of Institutional
agreements.
• I am not sure the status in India. University
research office or University library can take
the initiatives for open access agreements.

18. Open access journals
• List of Open AccessPublications Indexed by
Scopus
• Web of Science Master Journal List (Filter
option for open access journals)
• https://www.enago.com/academy/journal-
finder/ (certified by DOAJ)
• Scimago open access list

19. Managing your Research Profile

20. Research profile will help you to
Showcases your work to the world
Manages your publications list
helps to be identified by potential collaborators
helps to avoid misidentification
Enables your research output to be attributed to your university
Tracks citation counts
Enhances your University researcher profile page by including a link to other profiles

21. Recommended
researchprofile
platforms
ORCiD
ResearcherID
/Publoans
SCOPUS
author ID
Google
Scholar
profile

22. WHY IS
THERE A
PROBLEM?
• Name variations:
• Matthew J Buys, MJ Buys, M Buys, Matthew John Buys, ‫بايز‬
،
‫ماثيو‬

23. ORCID is free
Register for
an ORCiD
http://orcid.org/
Registration takes
only 30 seconds

24. How to add
your
publications
to ORCID
• SCOPUS
• WOS
• Crossref
• Google Scholar
• --- and more
You can add it from
The details are given in
https://zu.libguides.com/orcid

25. Google
Scholar
citations
• Google ScholarCitationslets authors set up a profile page that lists
their publicationsand citationmetrics.
• The citationmetrics are updatedautomatically,and you can choose to
have your list of publicationsupdatedautomaticallyor updatethem
yourself.
• You can sign up for a Google ScholarCitationsprofile:
• Sign in to yourGoogle account, or create one if you do not have
one.
• Go to Google Scholar and click on the My profile link.
• Follow the prompts to set up your profile and add your
publications.
• Review and complete yourprofile: for example, uploada photo
and double check the list of articles.
• Ensure you make your profile public if you want other people to
be able to view it.
• Visit your email inboxand click on the verificationlink.

26. SCOPUS
AuthorID
• A Scopus Author ID is automatically
generated the first time one of your
publications is indexed in Scopus.
• To find your SCOPUS ID, search for your name
or one of your indexed publications in
SCOPUS and go to your Author Details page,
where you will find your SCOPUS ID
• Due to variant publishing names Scopus may
generate multiple IDs for the same author.
Ensure you merge all your IDs to optimize
your citation metrics.

27. How to merge your SCOPUS IDs
• Click “Edit author profile” and follow the steps

28. Publons
from WoS
• The Publons is a free online systemthat provides
services for researchers to track and share their
research impact and contributions.
• The information about publications, citation
metrics from the Web of Science Core Collection,
peer-reviews and journal editing works of one
person can be located in one profile.
• Through the Publons, a researcher can express
his/her interest to be a reviewer for a journal
available in the Publons database.To have the
Publons profile, registration is required.

29. Publon
Mastering
peerreview
• Mastering Peer Review
• The Publons Academy provides a free online
training course to master peer review skills. The
course includes 10 modules. It is free and can be
completed anytime and from anywhere.
• Opportunities:
• Network with expert peer reviewers and
editors;
• Learning how the peer review process
works;
• Performing real reviews with mentor's
guidance;
• Endorsement by a mentor;
• Access to the reviews.

30. How publons
profile looks
like

31. Measuring the citation impact
of your research

32. Ways to Measure Impact
Your Impact based on citations to
articles
• Comprehensive Resources with
Citation Information
• Web of Science
• Scopus
• Google Scholar
• Above databases also calculate
the h-index
Altmetrics - Web 2.0 (Likes,
Tweets, Shares)
• total-impact.org(now called
ImpactStory); CitedIn
• Plos, Scopus

33. H Index
• An index to quantify an individual’s scientific research
output. J.E. Hirsch
• The h-index is based on the set of a researcher’s most
cited papers and the number of citations that the
researcher has received in other people's publications
• “A scientist has index h if h of [his/her] Np papers have at
least h citations each, and the other (Np − h) papers have
at most h citations each.”
• variants of h-index
• g-index
• a-index
• and more…

34. Calculating
H-Index
Article # - Times Cited
• 1-----87
• 2-----70
• 3-----46
• 5-----19
• 6-----15
• 7-----10
• 8 ---- 9
• 9 ---- 8
• 10--- 6
• 11---- 4
• 12---- 1
8 articles have been cited at
least 8 or more times and the
remaining articles have been
cited 8 or less
A scientist has index h if h of
[his/her] Np papers have at
least h citations each, and the
other (Np − h) papers have at
most h citations each

35. Author
citation
metrics in
Web of
Science
• Citation Analysis for a Known Author
You have two options for searing an Author.
1. Use Basic Search function and select Author
dropdown
2. Use Author search option
• Using the Search function, type the name of a known
author.
• On the results page, on the right hand side above the
results, click on Create Citation Report to see the
citation analysis for the author.
• The Create Citation Report option gives the numbers
for published items in each year, citations in each
year, total citations, average citations per item, and
the h-index.

37. Author
citation
metrics in
SCOPUS
• Click on Author Search.
• Type your last name, first name and affiliation
and click Search.
• Select the names that match your name.
• Click on Show Documents to see your
publications and how they were cited in Scopus.
• Click on Select All and then View Citation
Overview.
• You will see your H-Index.
• Scopusonly calculatescitationsreceivedsince
1996

39. Research Data Management

40. Whatis
Research
Data
Management
Research Data
• Data that are collected, observed, or created, for purposes
of analysis to produce original research results.
• Form of data: facts, observations, images, computer
program results, recordings, measurements or
experiences on which an argument, theory, test or
hypothesis, or another research output is based.
• Data may be numerical, descriptive, visual or tactile. It
may be raw, cleaned or processed, and may be held in any
format or media
Research Data Management (RDM)
• It covers the planning, collecting, organizing, managing,
storage, security, backing up, preserving, and sharing your
data and ensures that research data are managed
according to legal, statutory, ethical and funding body
requirements.

41. Why manage
research data
• Ensuring research integrity and reproducibility
• Increasing your research efficiency
• Ensuring research data and records are accurate,
complete, authentic and reliable
• Saving time and resources in the long run
• Enhancing data security and minimising the risk of data
loss
• Preventing duplication of effort by enabling others to use
your data
• Complying with practices conducted in industry and
commerce
• Facilitating the analysis of change, by providing data with
which data at other points in time can be compared
• Meeting funding body grant requirements (if applicable)

42. Research Data Management- Life cycle

43. FAIR principle

44. Research datamanagement-stages

45. Funding Agency requirements- Examples

46. Data
Management
Plan (DMP)
• A data management plan (DMP) contains all the
information related to managing the data for
your project: what data, stored where by whom,
how it is looked after and when it is made public.
• A researcher needs to make the plan in
compliance with funders and Institutional
requirements
• There are various tools and best practices guides
to help in this process

47. DMP tools
• DMP Tool (https://dmptool.org/) is a a free,
open-source, online application service of
the University of California Curation Center of
the California Digital Library.It helps
researchers to create data management
plans.
• DMP oline https://dmponline.dcc.ac.uk/ by The
University of Edinburgh
• RDM Plan Template - University of
Melbourne, Australia

48. Best practices of
Research Data
Management
• File organization & Formats
• Metadata
• Deal with sensitive data
• Data sharing
• Data citation

49. File structure
•Images fromthefield (.jpeg)
•Progress reports& presentations (.docx, .pptx& .pdf)
•Field observations (.xlsx & .csv)
•Analysis files & graphics (.xlsx& .R)
Types of data
•Date
•Collaborator
•Data collection method
•Location
•Data type
Include important contextual information
•The file naming should be consistent
•Try not to have very long file names (usually no more than 25 characters)
•Avoid special characters (i.e. ~ ! @ # $ % ^ & * ( ) ` ; < > ?. , [ ] { } ' " |) in a
file name
•Do not usespaces. Instead, herearesomealternative options: capitals (e.g.
FileName.xxx), underscores (e.g. File_Name.xxx)
•Use date formatYYYYMMDD or YYMMDD
•Includea version number
Include important contextual information

50. Metadata
• What is Metadata
Metadata is defined as "structured
information that describes, explains,
locates, or otherwise makes it easier
to retrieve, use, or manage an
information resource. Metadata is
often called data about data or
information about information.
Metadata Type Example
Properties
Descriptive metadata
Common fields which help users to discover
online sources through searching and
browsing
Title
Author
Subject
Genre
Publication
date
Technical metadata
Fields which describe the information
required to access the data
File type
File size
Creation
date/time
Compression
scheme
Metadata standards/schemas may vary from discipline to
discipline. Dublin Core is one of the most commonly-used
generic metadata standards.

51. Discipline specific metadata- Examples
• Agricultural Metadata ElementSet (AgMES)
• Astronomy VisualizationMetadata Standard (AVMS)
• Access to Biological CollectionData (ABCD)
• Institute of Electrical and Electronics Engineers (IEEE) Learning Object
Metadata (LOM) standard:
• More examples are available in Texas Tech University
https://guides.library.ttu.edu/c.php?g=765394&p=5697292

52. Sensitive data
Sensitive data can be information that is protected
against unwarranted disclosure. It can include but
not limited to personal data, proprietary data and
other restricted or confidential Data that should be
protected from unauthorised access.
Sharing Sensitive Information- Important points
• Including provision for data sharing when gaining
informed consent
• Protecting people's identities by anonymising
data where needed
• Considering controlling access to data
• Applying an appropriate licence

53. Data sharing
Important points
• Institutional Policies:
• Funder Policies:Researchers should be aware of any funder
policies that may stipulate the ways and restrictions on data
dissemination and sharing.
• ResearchCollaborationAgreement:Researchers should come
to an agreement on how, when, and by whom the data will be
accessed, used and disseminated in the future if appropriate.
• Usage of Extant ProprietaryData: Researchers should seek
permission from the data owner or producer prior to the
sharing the original or derived data if appropriate.
• Re-use of Others’Data: If the research data was not previously
collected by you, instead of sharing the research data,
researchers should give credit to the data producers with a
proper data citation.

54. Data repositories -
Directories
• Re3Data:Databaseof data repositories
• Fairsharing.org: Catalogue of databases and
related resources
• DataCite: Databaseof datasets and repositories
• European Union Open Data Portal: Catalogue of
open datasets
• DataCitation Index (DCI): Databaseof datasets
(TUoS access through the Library Web of
Science page)
• EMBL-EBI: Databaseof repositories and other
resources
• Google DatasetSearch

55. Data
repositories-
general
• Harvard Dataverse: by Harvard University
• Dryad Digital Repository: A broad life-sciences
and medicine repository to house data
underlying publications.
• Figshare: FigShare provides limited free storage
space to hold research data from various
disciplines.
• Mendeley Data: An open research data
repository by Elsevier, where researchers can
store and share their research data.
• Zenodo: A repository for research outputs from
all fields of science.
• https://ckan.org/

56. Subject specific repositories
• Chemistry
• Biological MagneticResonance DataBank
• Cambridge Structural Database (CSD)
• ChemSpider
• ChemSynthesis
• CrystallographyOpenDatabase
• PubChem
• ComputerScience
• CodePlexArchive:.
• Cooperative AssociationforInternetDataAnalysis(CAIDA
• GitHub
• Launchpad:
• SourceForge
• Earth and Environmental Science
• Climate Change Knowlegde Portal:
• National CentersforEnvironmental Information(NCEI)
• National Ecological ObservatoryNetwork(NEON)
• National SnowandIce Data Center(NSIDC)
• Geoscience
• Geospatial atData.gov
• Marine Geoscience DataSystem(MGDS)
• NASA'sEarthdata
• National Geospatial Digital Archive(NGDA)
• Biology and Life SciencesT
• he Cell Image Library
• Plant Expression Database (PLEXdb
• Universal Protein Resource (UniProt
• Worldwide Protein Data Bank (wwPDB):.
• Humanities
• Archaeology Data Service (ADS):
• ACultural Policy and the Arts National Data Archive (CPANDA)
• National Archive of Data on Arts and Culture (NADAC): TextGrid
• the Digital Archaeological Record (tDAR)
• Open Context
• Physics, Astrophysics and Astronomy
• HEPData:.
• National Nuclear Data Center (NNDC)
• NIST Atomic Spectra Database
• NoMaD Repository
• UK Solar System Data Centre (UKSSDC):
• Social Sciences
• Australian Data Archive
• Inter-university Consortium for Political and Social Research
(ICPSR):
• Qualitative Data Repository (QDR)
• UK Data Archive

57. Data
repositories
in India
• Many of the Indian scientificinstitutions have
their on Institutional repository system.Some
Institutions are archiving associated research
data also along with the theses and dissertation.
• There is only one repository came to my
attention where researchers can archive their
data
ICSSR Data Service

58. Thank you