Tuesday, August 22, 2017

Translating search strategies (updated)

This is an update of a post from November 2015.

If you are doing a systematic review, you will need to run the same search in more than one database.


I use the term "translation" for the process of modifying a search so that it works in another database.


It is important to run the same search in all databases.


So, if you have a search that works in Ovid Medline, what do you need to change to make it work in another database like PsycINFO or Embase?  Those other databases have different features or functionality.


There are three areas where translation is necessary, once you have finalised your strategy:


Search syntax – phrase searching, proximity, truncation, field searching
Subject headings
Limits



Here are some pointers.    For detailed help, consult the help files of the database itself.


Search syntax


Phrase searching


Ovid will assume that the keyword heart disease is the phrase heart disease. 
NHS databases, Cochrane, Web of Science and PsycINFO via Ebsco will not assume this and will treat the keyword as if it was heart AND disease.  To force a phrase search, put the phrase in double quotes (speech marks):


"heart disease".


Proximity operators
A proximity operator finds one keyword next to another, or one within a specified number of words of the other.


So, in Ovid Medline:


heart adj disease


finds the word heart next to the word disease, in that order.   (This is the same as searching for the phrase, of course)


heart adj2 disease


finds the word heart within two words of the word disease, so will find heart disease, disease of the heart.


You can use proximity operators with the truncation symbol (see below), so


heart adj3 disease*


finds heart disease, disease of the heart, diseases of the heart, diseases of the human heart.


Proximity operators in other databases are:


Ovid Embase and NHS databases - the same as Ovid Medline


PsycINFO via Ebsco - Nn finds one word within n words of the other, in either order.  Wn finds one word within n words of the other, in that order.


Cochrane - NEAR/n finds one word within n words of the other, in either order.  NEXT finds two words adjacent to each other (you cannot use truncation and phrase searching together in Cochrane, so this is an alternative).


Web of Science  - NEAR/n works the same as in Cochrane.  


Truncation and wildcards


Using a truncation symbol will find words that begin with that string of letters, so disease* finds disease, diseases, diseased...


I think * is the truncation symbol in most databases but check the help files.  Also check the help files to see how many characters the * can stand for.


Field searching


In Ovid you will see:


Heart.mp.


.mp. stands for the (article) title, abstract and some other fields and Ovid has searched for the word heart in any of these fields.   .mp. is the default for free text searching in Ovid.   To search just in titles and abstracts in Ovid, you can use .ti,ab.:


Heart.ti,ab.


Ovid Embase also uses .mp.   In other databases there is probably no exact equivalent of .mp.   To search for words in titles and abstracts, do this:


NHS databases: .ti,ab   (no second full stop)


PsycInfo via Ebsco - you can use the drop down box to select title, or abstract.   Not making a choice searches all fields, and this is the closest equivalent to .mp.


Web of Science - select Topic in the drop down box.   This is the closest match to Ovid's .mp.


Cochrane Library - (heart):ti,ab    You must put the search term(s) in brackets.  Note the colon and that there is no final full stop.  


Subject headings


Medline has subject headings, called MeSH, and you should use these in your search.   These subject headings are listed in a “thesaurus”.   In your search history they have a final /, for example Diabetes Mellitus, Type 2/.    Exp before the term means the term is exploded.  


Some databases do not have a thesaurus.  Some databases have their own, and so the subject headings may not be the same as those in Medline.


You need to take this into account when modifying your search.


Cochrane uses MeSH (but not in all databases).  Use the MeSH terms you used in Medline.  In the Search Manager, you can enter them like this:


[mh heart]


This will explode the term heart.  If you do not want to explode it, use ^, like this:


[mh ^heart].


If the MeSH term is a phrase, put it in double quotes:


[mh "diabetes mellitus"]


Web of Science has no thesaurus at all.  In a database without a thesaurus, I would ensure
I have searched for the MeSH term as free text.    You have probably done this anyway.


PsycINFO, Cinahl and Embase have their own thesauri.


Identify the term that is used for the concept you are searching, by entering the MeSH term or another keyword and exploring the thesaurus.    


If you have used explode in Medline, a good rule is to use it in other databases.


PsycInfo has more detailed terms for psychological concepts, and Embase for drugs and drug administration, so there may be thesaurus terms available that Medline does not have.  


Any thesaurus may have different terms from Medline, for example, the subject heading in Medline for type 2 diabetes is Diabetes Mellitus, Type 2/, and in Embase it is non insulin dependent diabetes mellitus/.


It may be too late to tell you now, but translating a Medline strategy is easier if you have MeSH and freetext on separate lines of the Medline strategy.


Limits


You may have used limits in Medline to find particular publication types, or work relating to a particular age group.


There are issues with limits and you might have used search filters instead (see this separate post).  If you have used a search filter, look for a version for the database you are
translating into.  


If you have used limits, check if those same limits are available in the database you are translating into.


Here are some things you should know:


Date and language limits are available in most databases.


There are detailed publication type limits in Medline, and also in Embase and Cinahl.   The definition of, say "randomised controlled trial" should be the same across the three databases but you might be wise to check.


PsycInfo has detailed publication type limits, and you should check that they match what you used in Medline.


Web of Science has no publication type limits beyond "journal article" and "review".    You would need to screen your Web of Science search results for references that match your chosen publication type.


The Cochrane Database of Systematic Reviews is of course all systematic reviews, so no limit needed.   The Trials database in Cochrane is all clinical trials (randomised and otherwise) so again no limit is needed.


Embase, Cinahl and PsycInfo have age group limits, but they might not be the same as Medline's (or each other's).  


Web of Science and Cochrane have no age group limits.

Monday, July 03, 2017

Onco-cardiology, or Cardio-oncology

I was at a Cardiology Education Meeting where a case was presented of a patient receiving a monoclonal antibody for melanoma, who may have then developed myocarditis.

Onco-cardiology (or cardio-oncology) is the study of the cardiac effects of cancer treatment but also used to refer to patients who are cancer survivors with a cardiac condition or people living with both conditions.

Though not a new term, I don't remember coming across it before.   

Here is some introductory reading:

Some recent freely available articles (with links to PubMed):







There is also a review from JAMA Cardiology (not free).

The American College of Cardiology and American Society for Clinical Oncology have pages about onco-cardiology.

Some Canadian guidelines on the evaluation of cardiovascular complications of cancer therapy are here.

A (freely available) 2013 European Heart Journal article about cancer drugs and the heart is here.

Wednesday, June 21, 2017

World Sickle Cell Day

Better late than not at all... 

Monday 19th June was World Sickle Cell Day and our local CLAHRC has been conducting a survey, which found that a greater awareness of sickle cell disease would improve patients' experience, and that staff in emergency settings had a relatively poor knowledge.

They have produced an infographic.

To improve knowledge, here are some resources (list also posted on the UHL Clinical Librarian blog):

Local

Professor Simon Dyson, De Montfort University,  especially the Resources and Information page, which lists UK organisations and resources for schools.  Professor Dyson has also produced some open educational resources.

Rest of the UK

Clinical Knowledge Summaries for an evidence based summary.

HealthTalk for patient experiences of screening.

NHS Choices for an overview and links to other NHS resources.

NICE material is included in the set relating to blood conditions - a clinical guideline (CG143) and a quality standard (QS58)

Sickle Cell Society - UK based patient support organisation

Rest of the world



emDOCS - The sickle cell patient: ED management of acute complications.   Detailed discussion from this US based emergency medicine blog.  

Life in the Fast Lane (LITFL) - Sickle cell crisis.  Another blog for emergency medicine and critical care, based in Australia and New Zealand.

MedGen for everything genetic.


Friday, June 16, 2017

ECG interpretation

In my last post I mentioned ECGs.

And as well as the book mentioned in the last post, there are the various books by John Hampton:

  • ECG made easy
  • 150 ECG cases
  • ECG in practice

Look for them in your library!

But there are limitations to books when it comes to teaching and learning interpretation of ECGs. 

That is pointed out on the ECG Wave-Maven site, used as the source of ECGs at the Cardiology education meeting I have just returned from:

Nathanson LA, McClennen S, Safran C, Goldberger AL. ECG Wave-Maven: Self-Assessment Program for Students and Clinicians. 


You can browse a case list, with or without diagnoses, or see a random case, and you can search for particular diagnoses.   If you like it on Facebook, you get notifications of new cases.

Here are some other sites about ECG interpretation.  Some I mentioned last time, some not.


ECG Learning Center, University of Utah 


Life in the Fast Lane, ECG Library 


Analysis and interpretation of the electrocardiogram, Queen's University School of Medicine (Kingston, Ontario)

ECG (EKG) interpretation, Oxford Medical Education (read this to find out more about them - not part of Oxford University or OUP).



ECGpedia - tutorials, a textbook, reference cards, case of the month...   maintained by Jonas de Jong, a cardiologist in Amsterdam, who is also involved with the Textbook of Cardiology wiki.  (Ook in Nederlands).

Wednesday, June 07, 2017

Heart Rhythm Week - things about arrhythmia

This week is Heart Rhythm Week, with a focus on identifying undiagnosed people who have an irregular heartbeat.

To see if you have an irregular heartbeat, you of course have to take your pulse, and the Arrhythmia Alliance have instructions and instructions for children, along with other educational resources.

Here are some other resources about arrhythmia:

For electrophysiology in general you could start with Dr John M, a Kentucky based cardiac Electrophysiologist.


And for ECGs of arrhythmias and other conditions, you could start with Life in the Fast Lane or Patient.info.

Now I can spell “rhythm” and “arrhythmia”...

Postscript: In the library I found "Making sense of the ECG", 4th ed., by Houghton and Gray.  in the list of resources are:

ECGpedia - tutorials, a textbook, reference cards, case of the month...   maintained by Jonas de Jong, a cardiologist in Amsterdam, who is also involved with the Textbook of Cardiology wiki.

ECG Learning Center, from the University of Utah School of Medicine, with an introduction to the ECG, images and tests. 



Speak to your librarian, if you have one, as the library will have books about this condition and about interpreting ECGs, a favourite topic at cardiology education meetings.   

Friday, May 05, 2017

Caves - the Leicester connection


There we were on a tour, by boat, of Speedwell Cavern in Castleton, and I was sure that the guide mentioned the University of Leicester, and Trevor Ford.  It was in connection with exploration to find out how deep the "Bottomless Pit" would have been before a lot of mining spoil was tipped into it in the 18th century.

So I conducted my own web based exploration.

Trevor Ford was a Senior Lecturer in Geology, starting when the University was still a University College, was had research and outside interests in Derbyshire, the Peak District and in caves and Blue John.

Dr Ford died earlier this year and you can read an obituary here.

He also identified a fossil fern found in Charnwood Forest, and, as it happens, was a student of geology in Sheffield.

Friday, April 21, 2017

Search strategy for chronic kidney disease

Chronic kidney disease?  Chronic kidney failure?   Chronic renal failure?

There are many ways to describe this (1).  After a few searches on the topic, I tried to come up with a Medline strategy.  I think it may include some conditions that Hsu and Chertow would not, but I have this:

1.            ((endstage or “end stage” or established or chronic or progressive) adj1 (renal or kidney) adj1 (failure or disease* or insufficienc*)).ti,ab
2.            (Chronic adj1 nephropath*).ti,ab
3.            (“Chronic uremia” or “chronic uraemia”).ti,ab
4.            (CKD or CKF or CKI or CRD or CRF or CRI).ti,ab
5.            (ESKD or ESRD or ESRF).ti,ab
6.            kidney diseases/ and chronic.ti,ab
7.            exp Renal insufficiency, chronic/ 
8.            Renal insufficiency/ AND chronic.ti,ab

9.            1 or 2 or 3 or 4 or 5 or 6 or 7 or 8

This is for Medline via HDAS.   

I started with terms I had used previously, and added terms used by colleagues at UHL, MeSH Used For, and terms used in strategies in First Consult, SIGN guideline 103 and NICE CG182.  I then asked people on lis-medical, and also had some further suggestions when I circulated the strategy there.

This, for the record, is the version dated 22nd June 2016 with tiny minor amendments made in April 2017 to remove some unnecessary full stops! 

(1) Hsu CY, Chertow GMChronic renal confusion: insufficiency, failure, dysfunction, or disease. Am J Kidney Dis. 2000 Aug;36(2):415-8.



Guidelines for comparing guidelines

This was asked at a writing workshop that  I led recently.   How do you go about comparing two guidelines?

Critical appraisal

Comparing is related to,  but not the same as, critically appraising a guideline, in which you are looking at guidelines individually.   Trisha Greenhalgh's very useful book How to read a paper has a chapter about appraising guidelines, with ten questions to ask about a clinical guideline.  There is also a systematic review of appraisal tools in this article in PLoS One by Ulrich Siering and colleagues.

Comparing

The National Guidelines Clearinghouse has a "Compare" tool.    You choose the guidelines you want to compare, by ticking a box in the search results list.  Then you choose which sections you want to compare, and you can then see on screen or in a spreadsheet, those sections side by side.   It takes the sections as they are, which means that you may be comparing very differently arranged texts.

A PubMed search for comparison clinical guidelines finds some papers that compare guidelines for specific conditions.  It also finds many papers about comparing other things, not comparing actual guidelines.  The search worked much better once I had corrected comparision to comparison although the wrong spelling still found a handful of things!

Missing out the word clinical, so comparison guidelines, finds more (and more irrelevant things too, of course).

Searching more specifically, for example comparison guidelines valvular heart disease, would of course be a way forward.

A quick look at MeSH headings for something old enough to have them suggests:

Practice Guidelines as Topic/ 
Comparative Study/.  

Searching those headings (type in practice guidelines as topic comparative study) together finds a lot of relevant looking papers that I had not seen before, (as they did not use the word "comparison"), amongst other papers comparing decisions or results related to recommendations in guidelines.    Combine this search with a clinical area or subject.

Reporting guidelines

Comparing is related to reporting guidelines too.  The AGREE Instrument helps assess the methodology of a guideline.  This is in the Equator Network Library along with the RIGHT Statement for reporting practice guidelines and some other things.

Thursday, April 06, 2017

Tears



One of the things about being married to a minister is that I sometimes end up helping with resources.    And so it was that I was asked how many tears someone would cry in a lifetime, for use as an illustration in a service.

This turns out to be a difficult question.  If you just count tears of sadness, then of course it depends on how often you are sad, and how sad, as well as how long you live.   But I ended up with a sort of answer, and although it was on the internet, it wasn’t found through a regular internet search.

I started with a regular internet search, for something like “how many tears are cried?”.  That brought up a lot of news stories, which give widely different figures, with no sources.

The chain of research then went something like this:

I found something from the Huffington Post, , and something from How Stuff Works.

These alerted me to the three types of tear (possibly a medical textbook would have told me that too).  Equipped with alternative search terms, I headed for PubMed.  I found this, searching for basal tear flow.

I then went back to Google, but Google Scholar.   I searched for basal tears volume, and along with the Farris article cited above, I found this from the British Journal of Ophthalmology from 1953.  That cites this 1903 paper by Schirmer.  I had no access to the full text of this but looking for it in Google finds this related article by De Roetth from the AMA Archives of Ophthalmology (related because it also cites Schirmer).     

De Roetth cites Schirmer but also mentions that Schirmer is citing work by Ahlstrom (also a related article to Schirmer in Google Scholar - 1895. Ahlström, Über die antiseptische Wirkung der Tränen. Zentralbl. f. Augenheilk. S. 193).   

I had no access to Ahlstrom either but de Roetth gives Alhstrom's figure (as well as describing the limitation of Ahlstrom’s method, which might mean the figure is too high).   The figure was 4 grams of basal tears a day.   De Roetth was not available in full online, but the first page, with this information, was.

I then made an assumption that 1g of tears was 1ml in volume, which was, I think, quite close, and another assumption about how long our hypothetical person would live.   Taking that as 80 years gave 4 x 365 x 80 ml of tears, which is 116.8 litres of tears in a lifetime.  

So, an answer for illustrative purposes.
 
And not a new answer.   A figure from 1895, cited in 1903, with that paper cited in 1953.  Although it did come up in an internet search, it was not found straight  away. 
Having read this far, you deserve this tear related song from my youth by The Beat, and then this one by Tears for Fears, with a video set in a library.

Monday, March 27, 2017

Syndemics

The Lancet has started a series about "syndemics" (may require a subscription).   Not a term I have come across before.   But not a new one, either.


It is to do with the interaction of diseases, and environmental and other factors.   The diseases or conditions have an influence on each other, and this is what differentiates syndemics from multimorbidity or comorbidity.


The term was devised by the anthropologist Merrill Singer, whose book Introduction to syndemics appeared in 2009.  Singer developed the "emergent concept" of syndemics "as part of an ongoing effort to rethink the public health and social scientific understanding of disease so that it focused attention on the multifaceted interactions that occur among the health of a community, political and economic structures, and the encompassing physical and social environment."  (Singer, 2009, p. xiii).  Singer was co-author of a paper in 2003 on the same subject, so definitely not a new subject, even if I have never heard of the word before!


Here are some other resources about syndemics:


Medical Anthropology Wiki.


A collection of articles on Co-Infection and Syndemics, from BioMed Central.




Syndemics Project, Florida International University.




Reference


Singer, Merrill, ed. (2009). Introduction to Syndemics.  John Wiley & Sons.



Wednesday, March 22, 2017

My pronouns are...

I recently saw an email, at the end of which was the statement:

"My pronouns are she/her/hers".

When talking about someone, for example, "go and talk to the librarian, and [pronoun] will help you", which pronoun do you use if you don't know the gender of that person?   If you use "he" or "she", that is gender specific and may not match the gender of the person.  "It" doesn't really work to refer to people.   I'd use "they".

But which pronouns would that person want used to refer to themselves?  That is what "my pronouns are..." is about.  Moves towards gender and transgender inclusion bring this issue to the foreground.  

There are resources like this poster from Vanderbilt University , which includes some  alternative pronouns ze/zir/zirs and ze/hir/hirs and advice on how to find out which pronouns a person prefers.    A search for "my pronouns are" from .edu sites brings up a lot more examples.   One, from University of California Davis  points to mypronouns.org, which goes into some detail and has "non binary, gender neutral" titles as well.

A search for .ac.uk sites finds a lot of grammar information about pronouns, rather less information about non binary gender neutral pronouns.   There is this from UCL.

But a search for the alternative term "preferred gender pronouns" finds a lot more from UK academic institutions, a lot of it from material about transgender awareness and support.

So, I am Keith and my pronouns are he/him/his, and I am off, linguistics degree (MA Hons 1986) and inclusivity in hand, to find out more.



Friday, March 17, 2017

We apologise for the delay to this blog...

Another long wait.

Caused by nothing specific.

I am going to try to get back in the writing habit.   This post does not count, though.