PubMed and other Online ToolsPubMed and other Online Tools

Michele R. Tennant, Ph.D., M.L.I.S.Health Science Center Libraries/

U.F. Genetics InstituteGMS 6014

tennantm@ufl.eduJanuary 2015

HSCL SessionsHSCL 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 ...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

EntrezEntrez• 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 OptionsEntrez 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 DifferencesEntrez Differences

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

controlled• Some archival, some curated

PubMed

PubMedPubMed• 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 PubMedTwo Ways to Get to PubMed• Directly at -

http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed

• Through HSC Library’s webpage:•http://www.library.health.ufl.edu/•Click on “Databases” icon•Click on “PubMed” icon

Controlled vs Non-controlled Controlled vs Non-controlled VocabulariesVocabularies

•“Old People” Example

Controlled VocabularyControlled 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 ExampleMeSH Example

• Find journal articles on the “physiology of membrane channels in mitochodria”

• Try the search again so that you discard peripheral articles.

• Search PubMed

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 apparentUse 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 OperatorsBoolean Operators

• Search statements may be combined using AND, OR, NOT

AND

OR 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 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 CaveatsMeSH 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 ArticlesMost 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 to E-journalsLink Out to E-journals

• 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 OMIM - Online Mendelian Inheritance in ManInheritance in Man

• http://www.omim.org/

• 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 #150330 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