Does MeSH on Demand have possibilities for identifying thesaurus terms for use in a search, as I wondered if in a previous post?
MeSH on Demand is here: http://www.nlm.nih.gov/mesh/MeSHonDemand.html. There is information about it in this NLM Technical Bulletin article.
As a first test, I entered this text:
The use of antibiotics to treat otitis media in children under 5.
MeSH on Demand suggests:
Anti-Bacterial Agents
Antibiotics, Antitubercular
Child
Dermatologic Agents
Humans
Otitis Media
There is a disclaimer that says that humans might have come up with different terms, and that MeSH on Demand might suggest terms that are not in the text, or miss ones that are. It does not assume any prior knowledge of MeSH.
I would have come up with the first and last terms, and humans, although I think that would be included implicitly if you include an age group. I would have chosen something more specific than Child.
If you explode the first term, Anti-Bacterial Agents, you would include Antibiotics, Antitubercular. There is no advice that I can see from MeSH on Demand about exploding. If you use PubMed, exploding would happen by default.
I would not have come up (at least, until I had examined some search results) Dermatologic Agents, so that is interesting and I would explore that.
There is no guidance from MeSH on Demand about how to combine terms. There is also nothing said about freetext terms that you might use.
As a second test, I input the abstract from an reference from PubMed, and the resulting list of suggested MeSH terms had a very small overlap with the actual terms applied to that reference. Indexers do look at more than the abstract, so there may be ideas in the article headings, conclusions and tables and figures that are not in the abstract. Interestingly, Philippines/ is suggested (it is mentioned in the abstract) but is not actually applied to the reference.
And as a third test, I used a search involving a drug and a condition that I had used as an example before. MeSH on Demand identified the disease MeSH term I had chosen, and a drug MeSH term I knew about but had rejected (as too broad), plus a MeSH Supplementary Concept (the idea of those was new to me, I have to say, and I am not yet sure how you search it in Ovid!) and a MeSH term for the part of the search I had decided to deal with by means of a publication type limit or filter. So in this case, MeSH on Demand was useful as a source of ideas.
Showing posts with label pubmed. Show all posts
Showing posts with label pubmed. Show all posts
Tuesday, August 04, 2015
Saturday, April 18, 2015
Medline, PubMed, or both?
A question raised in a recent teaching session with MSc students undertaking systematic reviews. Should I search Medline and PubMed?
Actually, people don't usually ask the question, but instead tell you that they have searched both, or that someone has recommended they do so, or that they have read a review where the reviewers have searched both.
I always say I am not convinced you need to search both. But am I right?
I know PubMed includes things that Medline does not:
1. Medline indexes some journals (like Science and Nature) selectively, and will not include non biomedical / life science articles. PubMed, however, does include them.
I don't think this would matter to a systematic reviewer in healthcare.
2. Issues of a newly accepted journal that predate the date when it was accepted for indexing in Medline will be included in PubMed. This might matter, but I have never been convinced that it matters enough to search both databases.
3. References sent from the publisher, but not yet indexed for Medline. This of course, might matter, but we have access to what used to be called "PreMedline", and what is now called "Medline In Process", which is these references. So, if your search includes freetext, you ought to find it without using PubMed.
But what about the fact that PubMed and Medline have interfaces that work in different ways? Is it possible to find material in one that you did not find in the other, just because of the way the search works? Surely if you search PubMed using the MeSH browser, and select the same MeSH terms as you did in Medline, you would find the same material. I have to say, that when I have been doing detailed searching for research projects (and this is not something I do a lot of, I do spend much more time teaching others to do it), I have never used PubMed, and always used Ovid Medline.
Here is a search that I did in Ovid Medline and PubMed. The syntax is Ovid's, and I used the MeSH browser and Advanced Search in PubMed to replicate it. The unexploded MeSH heading was not used in the results set, but I just wanted to check that PubMed had exploded the heading in set 1.
Actually, people don't usually ask the question, but instead tell you that they have searched both, or that someone has recommended they do so, or that they have read a review where the reviewers have searched both.
I always say I am not convinced you need to search both. But am I right?
I know PubMed includes things that Medline does not:
1. Medline indexes some journals (like Science and Nature) selectively, and will not include non biomedical / life science articles. PubMed, however, does include them.
I don't think this would matter to a systematic reviewer in healthcare.
2. Issues of a newly accepted journal that predate the date when it was accepted for indexing in Medline will be included in PubMed. This might matter, but I have never been convinced that it matters enough to search both databases.
3. References sent from the publisher, but not yet indexed for Medline. This of course, might matter, but we have access to what used to be called "PreMedline", and what is now called "Medline In Process", which is these references. So, if your search includes freetext, you ought to find it without using PubMed.
But what about the fact that PubMed and Medline have interfaces that work in different ways? Is it possible to find material in one that you did not find in the other, just because of the way the search works? Surely if you search PubMed using the MeSH browser, and select the same MeSH terms as you did in Medline, you would find the same material. I have to say, that when I have been doing detailed searching for research projects (and this is not something I do a lot of, I do spend much more time teaching others to do it), I have never used PubMed, and always used Ovid Medline.
Here is a search that I did in Ovid Medline and PubMed. The syntax is Ovid's, and I used the MeSH browser and Advanced Search in PubMed to replicate it. The unexploded MeSH heading was not used in the results set, but I just wanted to check that PubMed had exploded the heading in set 1.
|
Searches run 2230 BST 18.4.15
|
|||
|
|
|
Ovid Medline
|
PubMed
|
|
1
|
Exp Diabetes Mellitus, Type 2/
|
90273
|
88785
|
|
2
|
Diabetes Mellitus, Type 2/
|
90098
|
88612
|
|
3
|
Type 2 diabetes.ti,ab.
|
72369
|
72674
|
|
4
|
Insulin glargine.ti,ab.
|
1221
|
1234
|
|
|
(1 or 3) and 4
|
767
|
775
|
|
|
(1 or 3)
|
116064
|
115948
|
1542 references in total.
Using RefWorks to remove close duplicates leaves 795. Because author names are not
formatted the same, and journal titles in one database are abbreviated and in
the other not, finding exact duplicates did not identify many. However, the first pair of references (that is, a pair that RefWorks thought were duplicates) were not, which makes me wonder if I deleted items that were not duplicates.
So, there are a few references in PubMed that are not in Ovid Medline, and vice versa. I need to look in more detail at this to see why.
Removing large numbers of duplicates in RefWorks (I tell my students they can use RefWorks to manage duplicates when working on a systematic review) was interesting! I changed the default number of references per page to 500, or I would have had 50+ pages to deduplicate. I also looked at using EndNote Online to do this but it only seems to remove duplicates across the whole library, not a single folder, and as I had been using it for a real project, I decided not to do that.
Friday, February 05, 2010
Changes to PubMed
These changes, announced in a recent NLM Technical Bulletin, are now live:
"Limits" now appears as an option on the one line search screen - it did appear only on the Advanced Search screen for a while.
If you switch from one line to Advanced search, the one line search that you have been doing is now cleared - it used to stay there.
The Advanced Search screen will change - instead of the present three lines, with option to add more, there is a "search builder" - I had thought that this would enable you to add as many lines as you like, with the appropriate Boolean operators in between but in fact it seems to add your search terms to the basic search box, with the Boolean operators you choose. This seems a little like the "send to search box with..." that appears in the MeSH browser.
This post replaces the original, which had an inappropriate comment added that I could not work out how to remove.
"Limits" now appears as an option on the one line search screen - it did appear only on the Advanced Search screen for a while.
If you switch from one line to Advanced search, the one line search that you have been doing is now cleared - it used to stay there.
The Advanced Search screen will change - instead of the present three lines, with option to add more, there is a "search builder" - I had thought that this would enable you to add as many lines as you like, with the appropriate Boolean operators in between but in fact it seems to add your search terms to the basic search box, with the Boolean operators you choose. This seems a little like the "send to search box with..." that appears in the MeSH browser.
This post replaces the original, which had an inappropriate comment added that I could not work out how to remove.
Wednesday, November 19, 2008
More about PubMed
The NLM Technical Bulletin also describes some other changes - in the summary format, article title will appear first and be the link to a more detailed format, and the icons that denote full text or abstract available are going to disappear. There is a screenshot in the NLM Technical Bulletin article.
Changes to PubMed - advanced search
This, from the NLM Technical Bulletin, confirms that the tabs in PubMed are moving to the advanced search screen, and outlines some of the other changes that are afoot.
Advanced search (which I have to say I have not used a lot) is moving off beta and becoming... whatever things become after beta! Not gamma, I imagine.
Advanced search (which I have to say I have not used a lot) is moving off beta and becoming... whatever things become after beta! Not gamma, I imagine.
Monday, November 10, 2008
Changes to PubMed - advance information
A long gap since the last posting - apologies. I was in Mull for some of the time, but mostly it is just idleness and bad planning that has led to the silence.
PubMed now displays "clipboard" next to the search box, if you have added items to the Clipboard, and this is preparation for the retiral of the tabs. The possible implication, reading the NLM information, is that these features will go to the advanced search screen?
The "recent activity" box - cause of some debate on medical library discussion lists - can now be closed.
PubMed now displays "clipboard" next to the search box, if you have added items to the Clipboard, and this is preparation for the retiral of the tabs. The possible implication, reading the NLM information, is that these features will go to the advanced search screen?
The "recent activity" box - cause of some debate on medical library discussion lists - can now be closed.
Friday, September 26, 2008
New features in My NCBI - My Bibliography - updated
The My NCBI feature of PubMed has had some enhancements. There is an announcement about this, and yesterday afternoon (UK time) there was an announcement on PubMed that My NCBI would be missing for some hours while the changes were made.
The changes are there this morning (UK time!). My NCBI has a new look (and a new feel, doubtless). There is a "I forgot my password" feature, and you can elect to have your password remembered or to remain signed in at all times. The features that were there before are still there - saved searches, collections, filters - but there is now a "My Bibliography" feature, which appears with the collections and saved searches under "My Saved Data".
My Bibliography enables you to gather PubMed citations to your own publications. I tried this, for my own publications (all 2 of them!). You can choose more than one name, if you appear in more than one form, and the search box fills itself in, in the same way that the index boxes do, in PubMed itself, so you can see what forms of name exist within PubMed. You can apply filters - year of publication, grant number, and so on - and you could search by PMID. Once you have put your citations into My Bibliography, you can sort that list by title, first author and date, and you can remove citations.
You can add Other Citations to My Bibliography, this only searches PubMed and is designed to give you a place to collect other citations, not your own. This seems to suggest that there is no way to add citations that are not included in PubMed. There also seems to be no way to output the citations in My Bibliography into lists. There also seems to be no way to export from My Bibliography into things like EndNote, but since you can export from PubMed into EndNote, that seems not to matter a lot.
New bit - Laika Spoetnik has a posting about what happens if you try to save a search in My NCBI and that search has a line like #1 AND #2 in it. Read the posting if you have problems - and Laika suggests contacting the PubMed helpdesk as well, in case this is a bug.
The changes are there this morning (UK time!). My NCBI has a new look (and a new feel, doubtless). There is a "I forgot my password" feature, and you can elect to have your password remembered or to remain signed in at all times. The features that were there before are still there - saved searches, collections, filters - but there is now a "My Bibliography" feature, which appears with the collections and saved searches under "My Saved Data".
My Bibliography enables you to gather PubMed citations to your own publications. I tried this, for my own publications (all 2 of them!). You can choose more than one name, if you appear in more than one form, and the search box fills itself in, in the same way that the index boxes do, in PubMed itself, so you can see what forms of name exist within PubMed. You can apply filters - year of publication, grant number, and so on - and you could search by PMID. Once you have put your citations into My Bibliography, you can sort that list by title, first author and date, and you can remove citations.
You can add Other Citations to My Bibliography, this only searches PubMed and is designed to give you a place to collect other citations, not your own. This seems to suggest that there is no way to add citations that are not included in PubMed. There also seems to be no way to output the citations in My Bibliography into lists. There also seems to be no way to export from My Bibliography into things like EndNote, but since you can export from PubMed into EndNote, that seems not to matter a lot.
New bit - Laika Spoetnik has a posting about what happens if you try to save a search in My NCBI and that search has a line like #1 AND #2 in it. Read the posting if you have problems - and Laika suggests contacting the PubMed helpdesk as well, in case this is a bug.
Tuesday, September 23, 2008
Accessing full text journals via PubMed
This may be of interest to University of Leicester members. If you are at a different institution, then your access to resources may be different and you need to talk to your library.
Leicester now has a proxy server, which makes off campus access to databases and journals easier. PubMed, however, is not behind the proxy server.
What this means is:
- if you are on campus, and follow a link from PubMed to full text, that link will work if we have on campus access to the journal in question.
but
- if you are off campus, there is no way that the journal will be able to identify you as University of Leicester, and so very probably the link will not work...
...unless you do this...
- go to the Leicester Digital Library at http://www.le.ac.uk/library/digital/index.html and click the Login to electronic resources link.
- login with your CFS username and password
- you will then be taken to the A-Z list of databases
- go to P and choose PubMed
- follow the links as you would normally do. Now you are identifiable as University of Leicester, and so full text ought to work.
If you have any problems, tell me! Leave a comment on the blog or email me.
Leicester now has a proxy server, which makes off campus access to databases and journals easier. PubMed, however, is not behind the proxy server.
What this means is:
- if you are on campus, and follow a link from PubMed to full text, that link will work if we have on campus access to the journal in question.
but
- if you are off campus, there is no way that the journal will be able to identify you as University of Leicester, and so very probably the link will not work...
...unless you do this...
- go to the Leicester Digital Library at http://www.le.ac.uk/library/digital/index.html and click the Login to electronic resources link.
- login with your CFS username and password
- you will then be taken to the A-Z list of databases
- go to P and choose PubMed
- follow the links as you would normally do. Now you are identifiable as University of Leicester, and so full text ought to work.
If you have any problems, tell me! Leave a comment on the blog or email me.
Tuesday, August 26, 2008
PubMed's Drug Sensor
This was implemented in PubMed in mid August. Search for a drug that is included on a list of 200 or so, and on the Summary Results screen (the list of references), you will see links to other resources about the drug. Currently the link is to PubMed Clinical Q and A, which is one of the items on the NCBI Bookshelf.
This is a separate thing from what you see when looking at an individual item from a list of results, when there may be a link to more information about the drug in MedlinePlus, which will appear under a heading "Patient Drug Information".
More about Drug Sensor
This is a separate thing from what you see when looking at an individual item from a list of results, when there may be a link to more information about the drug in MedlinePlus, which will appear under a heading "Patient Drug Information".
More about Drug Sensor
Monday, July 14, 2008
PubMed includes DOIs
PubMed now includes DOIs in its records - see NLM Technical Bulletin article for more details. In the tagged MEDLINE format, the DOI is in a field called LID, according to this bulletin. I have done a quick PubMed search and found the DOI appearing as AID, however.
A quick test suggests that AID goes to the DOI field in RefWorks, and the Electronic Resource Number field in EndNote 9.
A quick test suggests that AID goes to the DOI field in RefWorks, and the Electronic Resource Number field in EndNote 9.
Wednesday, July 02, 2008
Changes to PubMed
Updated 14th July 2008
Lots of discussion about this on the MEDLIB-L list, and lots of detail of the changes on Laika Spoetnik's blog - Part III of her discussion is here with links to the previous two parts.
I wrote this, to go to the departments I liaise with:
1. The sidebar has gone from the summary results screen (to make way for “forthcoming features”. I don’t know what these are yet!). In some library circles this change is generating some controversy – if you don’t like it, let me know!
2. Advanced search. This allows you to search by field (author name, journal title, etc.), to set limits and to see your search history (limits and search history are available via the “old” routes too). Look for the “Advanced search” link next to the search box.
3. Changes to automatic term mapping (ATM). Previously, if you searched for a journal title or author name, but that title or name was the same as a MeSH term, you would get a subject search instead of what you wanted. To address this, a change has been made to the way ATM works. Previously, automatic term mapping would map your search terms to MeSH and to “text words” (words in titles and abstracts). It will now map to MeSH and “all fields”.
I think this might now introduce irrelevant references into your search, if your subject matches a journal or author name, but it does address the original issue. There is some controversy in library circles about this change, and so I would be interested to know if this has adversely affected your searches at all, or to have any comments. There are full details of the change at http://www.nlm.nih.gov/pubs/techbull/mj08/mj08_pubmed_atm_cite_sensor.html
New information about ATM: there is now a FAQ about it: http://www.nlm.nih.gov/services/pubmed_atm_change.html
4. Citation sensor: matches searches with citations if you use terms that can be interpreted as year, author name, journal title. Citation sensor results are displayed in a yellow area on the results display. This will not work if you use [au] and other tags in your search.
More details about citation sensor are at: http://www.nlm.nih.gov/pubs/techbull/mj08/mj08_pubmed_atm_cite_sensor.html
5. Title sort for results (does not ignore articles). Sorting results was possible before, but the title sort is new. You should know that it does not ignore initial articles, so a paper entitled “A new method…” will file under A, not N.
I have since discovered that the "old" spellchecker that used to say "Did you mean..." and offer a link to what it thought you meant has seemingly been replaced - I typed pharmacokinetics cucumin and it automatically told me there were zero results, but that it had searched pharmacokinetics curcumin instead, and showed me those results.
Lots of discussion about this on the MEDLIB-L list, and lots of detail of the changes on Laika Spoetnik's blog - Part III of her discussion is here with links to the previous two parts.
I wrote this, to go to the departments I liaise with:
1. The sidebar has gone from the summary results screen (to make way for “forthcoming features”. I don’t know what these are yet!). In some library circles this change is generating some controversy – if you don’t like it, let me know!
2. Advanced search. This allows you to search by field (author name, journal title, etc.), to set limits and to see your search history (limits and search history are available via the “old” routes too). Look for the “Advanced search” link next to the search box.
3. Changes to automatic term mapping (ATM). Previously, if you searched for a journal title or author name, but that title or name was the same as a MeSH term, you would get a subject search instead of what you wanted. To address this, a change has been made to the way ATM works. Previously, automatic term mapping would map your search terms to MeSH and to “text words” (words in titles and abstracts). It will now map to MeSH and “all fields”.
I think this might now introduce irrelevant references into your search, if your subject matches a journal or author name, but it does address the original issue. There is some controversy in library circles about this change, and so I would be interested to know if this has adversely affected your searches at all, or to have any comments. There are full details of the change at http://www.nlm.nih.gov/pubs/techbull/mj08/mj08_pubmed_atm_cite_sensor.html
New information about ATM: there is now a FAQ about it: http://www.nlm.nih.gov/services/pubmed_atm_change.html
4. Citation sensor: matches searches with citations if you use terms that can be interpreted as year, author name, journal title. Citation sensor results are displayed in a yellow area on the results display. This will not work if you use [au] and other tags in your search.
More details about citation sensor are at: http://www.nlm.nih.gov/pubs/techbull/mj08/mj08_pubmed_atm_cite_sensor.html
5. Title sort for results (does not ignore articles). Sorting results was possible before, but the title sort is new. You should know that it does not ignore initial articles, so a paper entitled “A new method…” will file under A, not N.
I have since discovered that the "old" spellchecker that used to say "Did you mean..." and offer a link to what it thought you meant has seemingly been replaced - I typed pharmacokinetics cucumin and it automatically told me there were zero results, but that it had searched pharmacokinetics curcumin instead, and showed me those results.
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