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Finding and Managing Scientific Information and Research Data

Chemistry and Biochemistry 2019

General Information

Assignment (to be submitted by 11:59 PM on February 18, 2020)

Instructions for the assignment in CHEM 232/2020 Spring

Assignment questions

Note: You can access the databases from links included in the assignment or provided on this course page under the tabs "Finding Literature" and "Finding Properties of Chemical Compounds." These links will take you to the location of the databases on the UMD Libraries site. You need to click, again, on the database link to access it.

Instructional videos related to the Assignment:

Scientific Fraud: Why researchers Do It?

Ethics in scientific publishing

McCuen, R.H. (2018) Advancing Scientific Knowledge: Ethical Issues in the Journal Publication Process. Publications 6, 1.

Greer, S. (2017). Elements of ethics for physical scientists. Cambridge, Massachusetts: MIT Press. (UMCP McKeldin LibraryQ175.35 .G75 2017)

Discovering and Managing Scientific Information

 

Resources for finding properties of chemical compounds

Name

What it is

Useful for

ChemSpider

Publisher: Royal Society of Chemistry (RSC).

Cost: Free

Chemical properties database. It provides text and structure searching to find compounds. ChemSpider SyntheticPages (CS|SP) extends this model to cover reactions.

CRC Handbook of Chemistry and Physics

Publisher: Taylor and Francis Group.

This is the Internet Edition of the CRC Handbook of Chemistry and Physics, which corresponds to the latest edition of the printed book.  Cost: License

Information about the chemical, physical and thermodynamic properties of chemical compounds.

PubChem

 

Publisher: National Center for Biotechnology Information (NCBI), National Library of Medicine. Cost: Free

 

Covers the chemical properties and biological activities of small molecules. Includes three linked databases: PubChem Substance, PubChem Compound, and PubChem BioAssay, which provide substance information, compound structures, and bioactivity data. Links from PubChem's chemical structure records to other databases such as PubMed.

Reaxys

 

Publisher: Reed Elsevier Properties SA. A web-based platform based on three chemical information databases: (Former) CrossFire Beilstein (organic chemical compounds), (Former) CrossFire Gmelin (inorganic) (and the Patent Chemistry Database (PCD).

Cost: license

An extensive repository of experimentally validated data, including structures, reactions and physical properties; contains pharmacological, eco-toxicological and toxicological data, specific bioassay results, and toxicity values; allows searching for substances by chemical name or by structure and reactions.

SciFinder

Publisher: Chemical Abstracts Service (CAS).

Cost: License

The CAS REGISTRY File allows finding millions of reactions, more than 1 billion predicted property values, more than 2 million experimental properties. Patent records from the major patent offices are available online within 2 days of the patents' issuance; combines sequences from CAS and GenBank databases.

The Merck Index

Publisher: Publisher: Royal Society of Chemistry (RSC).   Cost: License

An online reference work for information on chemicals, drugs and biologicals.

Bibliographic Management Programs

Program

Content and Features

EndNote Online

What is it? EndNote Online and Desktop bibliographic management program

Cost: EndNote Online is free with institutional license, with limited storage. The software version (EndNote Desktop) is for a fee, with no limitation for storage. (on a computer)

Features: Offers the highest number of citation styles. Excellent live technical support.

CiteYouLike

What is it? A service for managing and discovering scholarly references

Cost: Free

Features: Easily store references you find online. Discover new articles and resources. Automated article recommendations. Share references with your peers. Find out who is reading what you are reading. Store and search your PDFs.

Mendeley

What is it? Web-based and desktop bibliographic management and social media tool.

Cost: Free with limited web storage. Upgradeable for a fee.

Features: Simple interface; manages well PDFs. Retrieves metadata for retrieved PDFs. Performs also as a social media and collaborative tool

Overleaf

What is it? An online collaborative LaTeX writing and publishing tool 

Cost: free for individual use. For fee for collaborative or professional use.

Features: Compile your project so you can see the results right away. No need to install software. Real-time commenting and integrated chat allows you to discuss your work without having to switch to email, printed versions or any other tool. Use in rich text format with Word. 

Papers

What is it? Bibliographic management and collaborative tool

Cost:  Unlimited cloud storage for your personal library. Included in ReadCube.

Features: Web importing via browser. Built-in search engines. Includes advanced article metrics (e.g., citations). Highlighting and drawing tools. Text to speech tool. Includes ReadCube papers app.

ReadCube

What is it? A suite of web, desktop, and mobile reference management programs for finding, organizing, reading, sharing, and citing research literature. Includes ReadCube Papers app

Cost: Different pricing options

Zotero

What is it? Browser add-on for Firefox, Chrome, and Safari.

Cost: Free open source program. Free for limited web storage. Upgradable for a fee.

Features: Good documentation and user guides. Manages a variety of formats. Good functionality. Easy to download, use and export citations.

 
 

 Resources for datasets

Resource

Content and features

DataCite

 

Data registry, which allows finding a repository to deposit and/or find data. Assigns DOIs for datasets. Incorporates Databib (a catalog, registry, directory, and bibliography of research data repositories).

Data Citation Index

Single search interface for over 350 data repositories worldwide.

Data.gov

 

U.S. Government’s site for open data. Includes tools and resources to conduct research, develop web and mobile applications, and design data visualizations.

Digital Curation Centre (DCC)

Leading international center for data management located in the United Kingdom.

DataONE

 

Data Observation Network. Provides access to data across multiple member repositories, supporting discovery of Earth and environmental data.

Dryad Digital Repository

Curated resource that provides a home for a wide diversity of datatypes and makes scientific data discoverable, reusable, and citable.

figshare

Repository for many different kinds of files (e.g. figures, datasets, media, papers, posters, and presentations), which can be uploaded and visualized in a browser.

Google Dataset Search

Enables users to perform a simple keyword search to find datasets stored in thousands of repositories across the Web. Accompanies the search engine Google Scholar.

Harvard Dataverse Network

Repository for long-term preservation of research data. Provides permanent identifiers for datasets. Open to all researchers worldwide to publish research data across all disciplines.

Mendeley Data

Allows storing, sharing, publishing, and finding research data, Includes millions of datasets from domain-specific and cross-domain repositories.

National Technical Reports Library

A data publishing and discovery platform of the National Data & Surveying Services (NDS) Consortium hosted at the University of Illinois.

NIH Data Sharing Repositories

National Institute of Health-supported data repositories that make data accessible for reuse.

OpenAIRE

 

Open Access Infrastructure for Research in Europe. Large-scale shared archive network of aggregated digital repositories for datasets and other kinds of scientific outputs from many disciplines.

OpenDOAR

A global directory of Open Access repositories and their policies.

RDA

Research Data Alliance. International organization. Connects researchers. Enables open sharing of data across technologies, disciplines, and countries.

re3data.org

re3data.org is a global registry of research data repositories that covers research data repositories from different academic disciplines. It presents repositories for the permanent storage and access of data sets to researchers, funding bodies, publishers and scholarly institutions; funded by the German Research Foundation (DFG).

SHARE

 

SHared Access Research Ecosystem. OA research network of cross-institutional digital repositories; associates papers with datasets.

Using SciFinder

Using PubMed

Using Reaxys

Using EndNote Online

Using Zotero

General instructions for using Zotero

Zotero Quick Start Guide

Zotero Documentation

Zotero General Preferences

Using Zotero in FireFox: an overview

How to insert Zotero citations and references into a Word document

Getting Started with Zotero: Using Zotero Standalone

 

 

 Major STEM Publishers

Organization

Profile

American Chemical Society (ACS)

Nonprofit membership organization. Publishes almost 60 journals, as well as conference proceeding, and scientific databases (SciFinder and STN). It also organizes conferences.

American Institute of Physics (AIP)

Nonprofit membership organization. Publishes research journals, conference proceedings, magazines, books, and newsletters covering physics and related disciplines. It also organizes conferences.

American Physical Society (APS)

Nonprofit membership organization. Publishes research journals, newsletters, and magazines covering physics and related disciplines. It also organizes conferences.

Chemical Abstracts Service (CAS)

Division of the ACS. Publishes scientific databases: SciFinder and STN, which carry the Chemical Abstracts database (CAPlus), MEDLINE, and the Registry File. Other databases: PatentPak, CHEMCATS, Science IP, ChemZent, MethodsNow, and NCI Global https://www.cas.org/products

The Chemical Society of Japan (CSJ)

Professional organization and publisher. Publishes journals and books. It also organizes conferences.

Clarivate Analytics

Commercial publisher of scientific databases (Web of Science, InCites, Derwent Patent database, Journal Citation Reports, Essential Science Indicators),  and research tools (EndNote, Publons, Kopernio).

Elsevier

Interdisciplinary commercial publisher of journals, books, and series. Publishes databases (ScienceDirect, Scopus) and a bibliographic management and data-sharing tool (Mendeley). Reed Elsevier Properties SA. Reaxys

National Library of Medicine

The National Center for Biotechnology Information at the National Library of medicine (USA) publishes many freely available databases and other resources for finding literature and properties of chemical compounds.  PubMed is the most widely used database for biomedical literature.

NIST

National Institute of Standards and Technology (NIST) publishes journals and databases related to chemistry.

Royal Society of Chemistry (RSC)

Nonprofit membership organization in the UK. Publishes journals, books, and databases (ChemSpider)

Springer Nature

Interdisciplinary commercial publisher of journals, books, series, conference proceedings, databases, software, reference works, and protocols in print and online. SpringerLink is a comprehensive online delivery platform, providing easy access to millions of STM resources, which publishes also many open-access journals.

Taylor & Francis Group

Interdisciplinary commercial publisher of journals, books, and databases.

Thieme

Commercial medical and STEM publisher of books, journals, online products, and series.

Wiley

Interdisciplinary commercial publisher of scientific, technical, medical, and scholarly journals, books, series, encyclopedias, educational and training materials in print and online. Publishes many open-access journals.

Scholarly communication formats

Scientific communication formats

Alternative communication

  • Books, Book chapter
  • Clinical trials
  • Conferences
  • Datasets
  • Dissertations and theses
  • Journal articles (Research articles, Reviews, Editorials, Letters)
  • Patents
  • Preprints
  • Technical reports
  • Blogs, web sites, individuals’ web pages
  • News articles
  • Works posted on institutional repositories
  • Experimental data posted in repositories mandated by funding agencies
  • Personal sites and social media (Twitter, Facebook, Instagram, LinkedIn)
  • Reference management tools with social functions (Mendeley)
  • Researcher communities ( Academia.edu, ResearchGate, ResearcherID)
  • Researchers’ profiles on institutional web sites, social sites, Google Scholar
  • Search engines with author profiles (Google Scholar, Scopus)
  • University author profile pages
  • Listserv (CHMINF‐L: The chemical information sources discussion list)
  • Wikibooks Chemical Information Sources/
  • Chemistry Wikipedia Portal
  • Use reliable and authoritative sources for finding information.
  • Use appropriate key words to describe the topic of your interest.
  • Use natural language, when this option is available. Some of the indexed databases (SciFinder, for example) allow using natural language, which provides more context to what the user is looking for.
  • Arrange the keywords by their significance for the search. The order in which you type the keywords may affect the results.
  • Use a “wild card” such as an asterisk (*) to broaden the search, if you are getting few results.
  • Search for a specific phrase by including it in quotation marks.
  • Look at the search terms suggested by the indexing service.
  • For an unfamiliar topic, find first review articles. The review article reviews primary research articles and gives the “big picture” for the topic.  Citations included in review articles provide a quick and easy way to find the most important literature published on the topic.
  • Refine search results using filters.
  • Unique identifiers
  • Untangling authors’ names
 

Strategies for finding literature and refining the search results

Type of search

Search using

Examples

Topic

Keyword, Phrase, Index term, Natural Language1

Natural language search:

aspirin for prevention of cancer

Author/Editor

Author Name, Author identifier: ORCID

ResearcherID

Last Name,2 First name, Initial

0000-0001-7066-058X

rid/H-1969-2011

Document Type or

Classification

Books, Book chapter, Clinical trial, Conference, Dataset, Dissertation, Journal article, Patent, Preprint

Journal articles: Research article, Review, Editorial, Letter

Document Identifier

Digital Object Identifier (DOI), PubMedID, Accession Number, Title, Author, Publication Year

DOI:10.1021/jacs.8b12671

Accession Number: 2019:204380
CAPLUS

Publication Name

Journal Name, Volume, Issue, Title Words, Author Name, Publication Year

Journal of the American Chemical Society, J. Amer. Chem. Soc., JACS

Organization

Company, University, Organization, Institution

American Chemical Society (ACS)

1Search engines and indexing databases use stop words such as “and,” ‘of,” ‘with.” 2Some indexing databases (SciFinder) search for alternate spellings of author’s last name.

Types of databases

Academic search engines

BASE (Bielefeld Academic Search Engine), DuckDuckGo, Google Books, Google Datasets Search, Google Scholar, Google Patents, Mendeley, Microsoft Academic, re3data.org, Science.gov, Bing.com, regional search engines: Baidu, Baidu Academic,, so.com, x.mol.com

Indexed databases

Bibliographic

PubMed/MEDLINE, SciFinder and STN, Scopus, Web of Science, Academic Search Premier

Cited/Citing

Google Scholar Citation, Scopus, Web of Science

Full-text databases

Academic Search Complete (EBSCO), American Chemical Society journals, American Physical Society journals, PubMed Central, Royal Society of Chemistry (RSC) journals and eBooks, ScienceDirect, Springer Link

Properties of chemical compounds

ChemSpider, CRC Handbook of Chemistry and Physics, NIST databases, Reaxys, PubChem, SciFinder and STN, The Merck Index

Indexed elements

articles, conference proceedings, graphs, tables, images, DOIs, authors names, ORCID, Researcher ID

Level of indexing

Title, abstract, full text, references, figures, tables, images

TABLE 4. Bibliometric and full-text indexed literature databases

Name

Characteristics

Useful for

BioOne

Publisher: BioOne

Cost:

Time span:

Abstracts and Indexes, which provide access to peer-reviewed research

Coverage: biological, ecological, and environmental sciences.

EBSCO  Information Services

Publisher:  EBSCO

Multidisciplinary database

Cost: Paid  license

Time Span: 1965-present.

Includes titles compiled by the company as well as journals from other databases/publishers such as Medline and  EconLit. The company also maintains Academic Search Complete, which covers the full-text of journals.

Coverage: nearly every area of academic study. Includes a large collection of peer-reviewed full text articles.

Google Scholar

Publisher: Google

Cost: Free

An interdisciplinary search engine for finding scientific literature. Authors can create a personal profile, which will appear in the list of the search results when people search for this author’s name, if the profile is made public.Includes several citation metrics and shows graphically citation analysis data.

PubMed/MEDLINE

 

Publisher: National Library of Medicine (NLM). Cost: Free

Time span: mid-1960s – present.

Comprehensive resource for biomedical literature. Based on the MEDLINE database.

Covers extensively the chemical literature. The database underlying PubMed is MEDLINE, which uses a thesaurus (MeSH Index) to index documents.

PubMed Central (PMC)

Publisher: U.S. National Library of Medicine (NLM)

Cost: Free

Database of citations and abstracts of publications in the Life Sciences; a post-print repository for publications of work funded by the U.S. National Institutes of Health.

ScienceDirect

 

Publisher: Elsevier

Cost: Paid  license

Peer-reviewed, full text database containing electronic books, book chapters and journal titles in science, technology, and medicine. Extensive coverage of the physical and biological sciences.

SciFinder

 

Publisher: Chemical Abstracts Service (CAS), 26 a division of the American Chemical Society  (ACS)

Requires registration to use it.

Cost: Paid  license

The most important resource for chemists.  A platform that carries two very large databases for finding literature (CAPlus and MEDLINE) that can be searched simultaneously, as well as the largest database for properties of chemical, the Registry File. For finding biomedical/life sciences literature, but provides also good coverage of chemistry journals. Searches can be performed through three main search pathways: topic, structures, and reactions. Covers many document types such as journal articles, conference papers, books, dissertations, and patents.

Scopus

 

Publisher: Elsevier

The world’s largest interdisciplinary indexed database, which provides sophisticated tools for refining and analyzing the search results.

Cost: Paid subscription

Multi scientific abstract and citation database: journals, conference papers, trade publications, book series, patents. Indexes journals from the fields of science, technology, medicine, social sciences, and arts and humanities. It also provides research analysis and tracking tools. Displays “Mendeley readership statistics” for any article that was downloaded to the bibliographic management program Mendeley.

Springer Link

 

Publisher: Springer Nature

 

Online journals in Biomedical and Life Sciences, Chemistry and Materials Science.

Web of Science

Publisher: Clarivate Analytics

Cost: Paid  license

Based on the Science Citation Index Expanded. A multidisciplinary index covering the journal literature of the sciences, including agriculture, astronomy, biochemistry, biology, chemistry, computer science, materials science, mathematics, medicine, neuroscience, physics, plant sciences, and zoology. It is the best database for finding which papers have cited other papers. Cited references can be traced forward in time. The Web of Science Core Collection includes the Science Citation Index Expanded, Social Sciences Citation Index, Arts & Humanities Citation Index, Emerging Sources Citation Index, Book Citation Index, and Conference Proceedings Citation Index. Web of Science is also a platform that includes other databases such as Essential Science Indicators, and Journal Citation Reports.