PubMed and other Online Tools Michele R. Tennant, Ph.D., M.L.I.S. Health Science Center Libraries/ U.F. Genetics Institute GMS 6014 January 2015

HSCL Sessions Searching tips Entrez PubMed – journal literature OMIM – review articles Nucleotides, Proteins, RefSeq – sequence databases Gene – gene-centered information hub Taxonomy Browser – taxon-centered information hub Next generation literature mining tools

Effective Searchers... know the content of the database subjects, data types, years of coverage, curated vs. non-curated understand the structure of the database record structure, searchable fields, controlled vs non-controlled vocabularies, search keys understand searching options and tools thesaurus, limits, preview/index, AND/OR, related records, etc.

Entrez

Entrez Search tool on the NCBI website Contains a variety of databases: Nucleotide sequence; Protein sequence; Molecular structure; SNPs; Expression data; Journal literature Each “database” contains “records” Each “record” in database contains “fields”

Entrez Search Options Similar among the various databases Entrez conventions: AND, OR, NOT, * Three ways to search: Basic: just enter your search terms Advanced: more controlled search - uses limits, preview/index, history Complex Boolean: command language with qualifiers in brackets; syntax= term [field] AND term [field] etc.

Entrez Differences Differences among the various databases Different search fields available Different limits available Some controlled, some non-controlled Some archival, some curated

PubMed

PubMed Journal literature database “Indexed” from 1946 on (but includes older non- indexed articles) Over 23 million records; almost 6,000 journals International in scope and language Pre-clinical and clinical information Most citations include abstract Takes advantage of controlled vocabulary search (better than keyword alone) Multiple subsets - MEDLINE, In Process, Publisher- supplied

Two Ways to Get to PubMed Directly at - PubMed PubMed Through HSC Library’s webpage: Click on “Databases” icon Click on “PubMed” icon

Controlled vs Non-controlled Vocabularies “Old People” Example

Controlled Vocabulary Controlled terms act as “umbrella” to pick up all synonyms, spelling differences (hemoglobin/haemoglobin), singular vs plural, etc. In PubMed, use MeSH Database to find and search controlled MeSH terms (Medical Subject Headings) Once in MeSH Database, can use additional options to enhance search (major heading, subheadings, etc.)

MeSH Example Find journal articles on the “physiology of membrane channels in mitochodria” Try the search again so that you discard peripheral articles. Search PubMedPubMed

Enter PubMed through our direct link (rather than through NCBI) and you will be able to directly see if the HSCL owns the journal articles you find

The “ufhsclib” indicates that you have entered PubMed correctly, and that the journals the library owns will be apparent Use the MeSH Database as a dictionary to find the appropriate MeSH term, and then to refine your search

Note that we have left PubMed and are in the MeSH “dictionary” You typed “membrane channels” into MeSH database This tells you to use “ion channels” rather than membrane channels

Topical subheadings help focus search to one or more aspects of the subject Check here and your topics will be the main point of the articles you find – you won’t get peripheral citations. Not recommended the first time you search a topic – if there are few papers in existence for your topic, you may be left with no articles at all

Note that the term “ion channels” will pick up all the more specific types of ion channels If you searched on any of these terms in MeSH, you would be led to the MeSH term “ion channels”

2. MeSH then automatically builds the search for you – in this example, you are looking for papers in which the physiological aspects of ion channels are the main point of all the articles you retrieve 1. Add your search to the Search Builder 3. Click “Search PubMed”

Once you have added the search to the Search Builder, and clicked on “Search PubMed”, you leave the MeSH Database, and the search is performed in PubMed Note that this is the search the MeSH Database built for you – it used the MesH term “ion channels”, glued “physiology” directly to the search by using the slash, and picked up all the different types of ion channels. MeSH also retrieved only the papers where these topics were the main points of the articles. You did not need to do any of this yourself – MeSH did it for you once you found the proper MeSH term, and clicked on subheading. Now we need to complete the second half of the search – mitochondria

Now we need to complete the second half of the search – mitochondria. Pull down the drop-down so you are in MeSH again, and search for the MeSH term. Look through the list to see if there is one that is most appropriate. Since we did not specify which type of mitochondria, we can choose the general term “mitochondria”. Read the “scope note” to be sure which term to choose. Scope Note

As in the membrane channel search, you can choose a subheading and limit to articles where this topic is the main point; I’ve chosen not to do so here, as the search did not specify it (if you don’t choose subheadings or main point, remember to click on the check box next to “mitochondria”). Send to search box; click “search PubMed”

You’ve now found articles on mitochondria, but you need to combine the ion channel with mitochondria concepts

Boolean Operators Search statements may be combined using AND, OR, NOT ANDOR NOT

To combine searches, choose “Advanced Search” The Advanced Search screen displays your PubMed history; from here you can combine your two searches using the appropriate Boolean operator

Results of our combined search. You have now found papers in which the physiology of membrane channels is the main point of the article. Each of those papers is also about mitochondria. Click to broaden search

MeSH etc. MeSH Database: Found appropriate search terms Automatically exploded “mitochondria”, so narrower terms (“mitochondria, muscle”, “mitochondria, heart”, etc) were ORed together Allowed the addition of subheadings (physiology) to narrow to a particular aspect Allowed narrowing to “main point” (throw away peripherals) Use History to combine (AND)

MeSH Caveats Performing a MeSH search is usually more precise and exhaustive than a keyword search, however: The most recent papers are not searched - therefore should also complete a keyword search “in process” Very new concepts/scientific terms may not yet be represented by MeSH Very specific or rare concepts may never be represented by MeSH So sometimes you will need to do a keyword search as well

Most Current Articles To find the most recent papers – can’t use MeSH Must perform a keyword search OR together synonyms, singular/plural, spelling variations Use * for truncation Don’t re-search the entire database – just the parts without MeSH: AND inprocess [sb]

Link Out Link Out to E-journals Link Out Remember, if you entered PubMed directly from the HSCL’s icon, you can see if the HSCL owns the journal articles you found Choose the “abstract” or “citation” displays from the pulldown menu Blue icons tell if the HSCL owns that journal issue in print Will NOT tell you what is available at Marston Science Library

Change display settings to “abstract” view to see journal icons Journal links Click to broaden search

OMIM - Online Mendelian Inheritance in Man Catalog of human genes and genetic disorders 22,745 records (as of 1/13/15) Records are basically “review articles” Records link to PubMed, sequences, structures, etc. Search tips: Look for your disease in “title” field on from advanced search If your disorder is listed as a phrase, put phrase in quotation marks

Choose the “Advanced Search” option for “OMIM”

x Limit so that your term(s) reside only in the “title” We will search for information on “lmna”, but first we limit so that we search only in the title field

This is a phenotype (trait, disease, disorder) record The other two records are gene records, and provide primary information on genes and proteins.

Table of Contents for this disorder Official OMIM Number Official OMIM Title You can often easily see which gene when mutated causes the disorder

Click on the OMIM # from the text of the phenotype record, and you end up at the gene record

Note that if the name of your disorder is a phrase, you will need to use quotation marks in your advanced search