Field qualification in PubMed

There are several ways to search for information in specific fields in PubMed.

The first is to click on the Preview/Index tab located under the query line. Next, select the field that you want from the All Fields drop down. You can then either choose Preview to add the word to the query box or Index to view the word within the alphabetical index.

The second way is to identify the field code or tag and using the appropriate syntax, enter the word(s) on the PubMed query line. While many tags are the same in Ovid and PubMed, some are different.

Here are a few examples:

pizza[ti] AND 2000[dp]
smith[au] AND yale[ad]

Where do you find the field codes or tags?

In the PubMed HELP under Search Field Descriptions and Tags.
And here's a translation table I put together that might help.

Dababase Highlight: Health and Psychosocial Instruments (HaPI)

This database is just the thing when you're looking for measurement instruments in health, psychosocial sciences, organizational behavior and library and information science. It covers questionnaires, interview schedules, checklists, index measures, coding schemes/manuals, rating scales, projective techniques, vignettes/scenarios and tests.

Be aware, however, that you're not going to find access to the actual instruments -- instead, you'll find citations to proprietary instruments as well as instruments that have only appeared in the journal literature or other reports (published or unpublished). And this is a case where you'll need to obtain copyright permission to use any of these instruments.

FYI:
If you're having difficulty locating instruments, tests or measures, try asking your friendly librarian. Chances are she's been asked this type of question many times before and has quite a few tricks up her sleeve.

Just the Facts
Available from Ovid
Updated quarterly
1985 to present, with some older material
Indexing and abstracting service (points to primary and secondary literature)
Produced by Behavioral Measurement Database Services
HaPI (Ovid Field Guide)

Let's talk field qualification

Field qualification is an excellent way to make use of the individual fields that make up a record within a particular bibliographic database (MEDLINE, CINAHL, PsycINFO,Science Citation Index, etc). And the reason that you would want to is that this method allows you to instruct the system to look for exactly what you want in the very field that you expect it to be. How powerful!

So each record within the bibliographic database has individual fields. Examples of fields are: Author, Title, Journal, Volume, Issue, Pages, Abstract, Institution, etc.

Usually, the search interface for the database will allow you to do field searching in several different ways. Let's use Ovid as an example (later we'll talk PubMed and Web of Science).

In Ovid, you have the option of using 'Search Fields' icon across the top (above the search history box). Clicking on this icon will bring you to the Search Fields page. Here's where the fields (and their two letter codes or tags) are listed. Check as many fields as you want and type the word you're searching for in the query box. Then choose between Perform Search and Display Indexes. Display Index(es) will actually list your word in an alphabetical index with an indication of what field it came from. I use this frequently when I'm unsure of the spelling of a word or when I want to see all the variations of the word as it is used in the database.

The shortcut method is use command language in the query box and for that you need to know the two letter code (aka field tag) for the field and the appropriate syntax. Here are some examples:

diabetes.ti. and 2005.yr.
schizophrenia.ti. and 2004.yr. and 649.pg.

Optimal search strategies for systematic reviews

Here's an article that describes optimal search strategies for retrieving systematic reviews in MEDLINE.

Article:
Optimal search stratigies for retrieving systematic reviews from MEDLINE: analytical survey.

Victor M. Montori, Nancy L Wilczynski, Douglas Morgan, R. Brain Haynes for the Hedges Team
BMJ 2005; 330; 68-; originally published online 24 Dec 2004.
doi: 10.1136/bmy.38336.804167.47 (published 24 December 2004)

FYI: These strategies are part of the Clinical Queries in Ovid MEDLINE. To utilize these filters, first complete your topical search. Click on the Limit icon, scroll down the page until you come to the Clinical Queries box, highlight the appropriate filter, and then click the Limit button.

Identifying the right Author in a sea of common last names

In previous posts, I’ve mentioned tips for author searching using truncation. But what do you do when the author has a common last name?

Here are a few things to try!

1. You know the author’s last name and an institutional affiliation

[Ovid] smith $.au. and yale.in.

[PubMed] smith *[au] AND yale[ad]

2. You know the author’s last name, an institutional affiliation and a potential department

[Ovid] smith $.au. and yale.in. and cell biology.in.

[PubMed] smith *[au] AND yale[ad] AND cell biology[ad]


** For both the above, once you’ve found an article by the RIGHT author, go back and do a targeted author search using the initial, initials, or initial truncated that you’ve identified. **

3. You KNOW the author’s full name but there are many authors with the same last name and the same initials.

This last thing to try is just for MEDLINE. It’s based on the Full Author field which was added to MEDLINE in 2002 so this works best if your author published after 2002


[Ovid] After trying any combination of the above and you’ve identified an article that you believe is the right one but want to verify. Click on the ‘Complete Reference’ link. Notice that right under the ‘Author’ field is the ‘Authors Full Name’ field. (if you still see initials in that field, I’ll bet the article was published before 2002)

Another trick for Ovid is to search the ‘Authors Full Name’ field first.
smith john.fa.
smith james $.fa. and yale.in.

[PubMed] After trying any combination of the above and you’ve identified an article that you believe is the right one but want to verify. Change the Display drop down from ‘Summary’ to MEDLINE and click on Display. Scan through the record until you come to the FAU and AU field tags and that’s where you’ll find the author information.

In PubMed the FAU field is a display only field. It is NOT searchable. Ovid has made the Full Author field searchable.

---

au is the author tag
.au. is the syntax for field qualification in Ovid
[au] is the syntax for field qualification in PubMed
in is the institution or address field tag in Ovid
ad is the institution or address field tag in PubMed
fa is the full author field tag in Ovid
* is the truncation symbol in PubMed
$ is the truncation symbol in Ovid

PsycINFO Cited Reference Searching [Ovid]

In the new reload of Ovid’s PyscINFO, you should notice links from the Cited References to the associated PsycINFO bibliographic record.

Now, if you’ve never noticed the ‘Cited References’ in PsycINFO, you’re
missing a treasure trove of information – this is a great way to expand the
scope of a subject search to find additional relevant articles that may have
been missed in a standard subject search. You can think of cited references the same as the reference list or bibliography of an article.

Where are these ‘Cited References’?
Once you’ve completed your subject search in Ovid PsycINFO and are looking at
the search results, identify a particular article that you are interested in
and click on ‘Complete Reference’. On the next screen that appears, scroll to
the end of the record and the Cited References will be listed. Notice that some of the cited references have links, some that work more successfully than others. Ovid is working on improving the linking problem. Watch the blog for further developments.

Default Operator - What's that all about?

So, you're looking for a two or more word phrase either in a search engine or in a proprietary database. Let's use the phrase ice cream headaches.

The default operator usually refers to the Boolean or positional operator the system has been instructed to apply between the words. And it makes a big difference in the retrieval...

Ovid and the Web of Science, for example, have a default operator of adjacency. Adjaceny forces the system to look for the word 'ice' to be adjacent to the word 'cream' to be adjacent to the word 'headaches'. This is the tightest relationship possible between these three words.

Web search engines, as you've probably discovered, mostly have a default operator of AND. By checking the HELP or Search Tips for your favorite search engine, you can discover the appropriate technique for ensuring that the phrase you're looking for is actually searched as a phrase. Usually the technique is to enclose the phrase in quotation marks, like this: "ice cream headaches".

Author! Author [PubMed]

Here are some tips for searching authors in PubMed.

First, remember the author field follows this syntax:
glover jg (Last name, first initial second initial)

Using the query box, type in the author last name and first and middle initial:

glover jg

If you don't know the middle initial, simply type in the query box: last name first initial. PubMed will retrieve records with the last name, first initial, any middle initial, or no middle inital.

If you don't know any initials at all, then it's best to use the author field qualification tag to restrict the search to the author field only. Type in the query box:

glover [au]

Otherwise, if you typed glover in the query box without the author field qualification tag, PubMed would find Glover Hospital in the affiliation field.

Another way to do an author field qualification search is to use the 'Limits' tab. After typing the last name in the query box, click on the 'Limits' tab and then select 'Author' from the 'All Fields' drop down.

Truncation

Did you know that each database/search interface/ search engine has its own truncation symbols?

These handy dandy symbols help when you either choose to bypass a controlled vocabulary in favor of textword and phrase searching or you must use textword and phrase searching since the system is not based on a controlled vocabulary.

Textword and/or phrase searching relies on you (yup, you!) to accommodate for all variations in word endings. And the best way to do that is to use the truncation symbol. Here are some examples:

Ovid
$ unlimited number of characters [computer$.ti.]
$n restrict retrieval to indicated number of characters [computer$3.ti. retrieves computer or computers or computerize, but not computerization]

PubMed
* unlimited number of characters for the first 600 variations of a truncated term [computer*]

Web of Science

* unlimited number of characters [biolog* retrieves biology, biologist, biologists, biological]

Orbis

? unlimited number of characters [environ? retrieves environment, environmental, environs]

Now where do you find out what the truncation and wildcards are for a new database?

Check the HELP screens! It’s all revealed right there.

Author! Author! [Ovid]

Searching for authors can be tricky but these tips can really help.

First, figure out what the syntax is for authors in whatever database you’re searching. For example, in MEDLINE and in CINAHL the author field follows this syntax:

Glover, JG (Last name, first initial second initial)

But in PsycINFO, the full author name is used:

Glover, Jan (Last name, first name middle name)

Not knowing that can cause some rather frustrating moments as you search for the author using the wrong syntax for the database you’re in.

One way to find out the correct syntax for the author field is to search on any keyword and examine the list of authors for the first citation that comes up.

Here are a few more tips:

When you’re unsure of an author’s full name and you’re using the ‘Author’ icon, make sure you choose every permutation of the name. Sometimes authors use their middle initials and sometimes they do not. So if you’re sure the author is 'Jan Glover' but you don’t know if she uses a middle initial, you would need to select all from the following list:

Glover, J
Glover, JB
Glover, JG

A shortcut would be to use a field qualification search on the command line:

Type: glover j.au. [retrieves all articles by the author with the last name Glover and first initial J and no middle initial]

Type: glover jg.au. [retrieves all articles by the author with the last name Glover and first initial J and middle initial G]

Type: glover j$.au. [retrieves all articles by Glover and first initial J with any middle initial]

Type: glover $.au. [retrieves all articles by anyone with the last name Glover]

au is the two letter code for the author field
.au. is the syntax that instructs the system to look for what ever is before this in the author field
$ is the truncation symbol in Ovid

It all starts with a question...

Over the past week, I’ve consulted with three people who were having difficulty finding information on their topics. After talking with each of them about what they tried, what terms were used and what they thought the problem was, it was clear that each would benefit from identifying what they really wanted and then framing that need in the form of a question.

When you begin a search for information, whether it’s a complex clinical situation or you’re trying to find a place to stay for an upcoming vacation, the process will be much easier if you begin by formulating a question.

It helps you think clearly and concisely about exactly what it is that you are looking for. A question helps clarify and direct your inquiry and because questions need answers, hopefully they propel you into action.

The question usually gives you clues on where to find the answer – a textbook, journal article, general database or a specialty database such as MEDLINE, PsycINFO or CINAHL.

From the question, you can also identify and prioritize the separate concepts that need to be searched – and indicate the relationships between the concepts.

If you’re having trouble with a search, make sure that you have a very specific question that you’re trying to answer. Sometimes talking it out with a colleague or your friendly librarian helps organize your thoughts and the question becomes obvious.

Finding the right Medical Subject Heading (MeSH) using PubMed

A colleague said to me, after reading the last post, “What about in PubMed?”

The same holds true for PubMed and here’s how to do it.

As you’re looking through the titles of your search results, pick one that seems the closest match to what you’re looking for. Then, click on the list of authors link to display the ‘abstract’ format of the reference. Notice that on the ‘Display’ line that ‘abstract’ now appears. Click on the drop-down and select ‘citation’. This is the display format where the MeSH terms appear.

Another way to do this from the Summary page is to check the box next to the pertinent title, click on the drop-down and select ‘citation’.

Sometimes there aren’t any MeSH terms. What’s up with that?

This usually happens when the citation is really recent or it’s a citation supplied by a publisher and you can tell by simply looking at the end of the citation on the PubMed Summary page.

If you see [PubMed - in process] then the record will only have basic citation information and abstracts until the citations are indexed with NLM's MeSH Terms and added to MEDLINE.

If you see [PubMed - indexed for MEDLINE] then the MeSH terms, publication types, GenBank Accession numbers, and other indexing data have been added to the record.

If you see [PubMed - as supplied by publisher] then these citations were received electronically from publishers. Most of these progress to "in-process" status and later to "indexed for MEDLINE" status. However, not all citations will be indexed for MEDLINE and therefore will retain either the tag [PubMed - as supplied by publisher] or [PubMed].

So, now give this a try in PubMed!

Finding the right Medical Subject Headings (MeSH)

If you’re having trouble finding the right Medical Subject Headings (MeSH) try this.

First, as you’re looking through titles of your search results, pick the title that seems the closest match to what you’re looking for. Then, click on the ‘complete reference’ link.

Scroll down through the record until you come to the ‘MeSH Subject Headings’ field. These are the terms that have been used to describe the subject content of the article. Examine the list for possible terms that you might not have thought of – or terms that really get at the concepts that are part of your research or clinical question. Make notes on all the possibilities.

Then go back to the ‘Main Search Page’ and type in the new terms you’ve just discovered.

Combine these new sets appropriately with your other sets. Use ‘AND’ to make that happen. Here’s an example of using an ‘AND’:

1. pregnancy in adolescence (4472 in this set)
2. exp obesity (59430 in this set)
3. 1 and 2 (22 - intersection of sets 1 and 2)


Give it a try!

Welcome to my search tips blog!

I'm hoping that I can help you keep your information seeking skills up to date by posting searching tips and techniques.

Since I'm a medical librarian, I'll be focusing mostly on databases such as MEDLINE (via Ovid or PubMed), PsycINFO, Web of Science, and other health and biomedical resources. But whatever comes to my attention that's interesting or cool, I'll bring to your attention.