PubMed: Past, Present And Future, PART I

11 06 2008

I.The Past:
Extremely simple, yet incredibly difficult

For Part II (discussion ATM, Advanced Search beta: see here).

Searching PubMed has never been easy, not for the advanced searcher nor the beginner.

As an advanced searcher you have (had?) to find your way through the Search Bar, MeSH-database, look for broader, narrower or related terms, know when to explode MeSH, add major topics or subheadings or not, know when to use ‘Links’ or the ‘Search to Sendbox’ to send Searches to PubMed. Know when and how to use Clinical Queries, Limits, Field Codes (nowadays called tags :) ), History, MyNCBI saved searches and collections, linkouts, AND, OR, NOT and so on….

It takes some investment of time to become an effective & advanced PubMed searcher.

For the less experienced and/or more rushed people (busy clinicians, young investigators, lab-people) trying to find an answer to medical questions, the search bar often sufficed. Here you just typed in some words that were not only searched in title and abstract, but also translated into the corresponding MeSH (if recognized as synonyms), a process called automatic mapping. People just haved to check “Details” to verify proper mapping. It often went well, but sometimes the mapping was completely wrong (i.e. typ: walking aids and you will search for the MeSH term for AIDS, although HIV has nothing to do with it).

The overwhelming number of hits could be effectively reduced with some risk of loosing relevant hits by using the Limits option or using Methodological Filters in the Clinical Queries (EBM). Because of the disease-oriented MeSH, PubMed is not very well suited for preclinical or basic scientific searches. This often leads to frustrations (see below).

Some people just want to look up citations and there is a perfect tool for it: the Single Citation Mapper. It is so wonderful, just type in an author, the journal, first page or whatever. It has an autofill function, so I even prefer this tool to find a journal or an author (instead of the indexes, which is yet another option).

Now let alone the summing up of these possibilities makes me see stars. After a course PubMed a student who knew a lot about programming, sighed:

Wow, there is a lot of stuff in there, but it is all so concealed and difficult to find….”

That’s true, and this together with the superficial resemblance of the search bar with the Google search bar makes inexperienced users use PubMed in a Googlish way: just typ in some words ….. and you probably… don’t find what you want. This was especially true for people looking up a particular paper and not familiar with the Single Citation Mapper, hidden in the blue side bar. (The picture left is from “Arts in Spe”, with the Title: Searching like in Google”)

Or as the Harvard PhD student Anna Kushnir expressed her frustations when ranting against PubMed :

“I hate PubMed. I hate it with a burning passion. For a site that is as vital to scientific progress as PubMed is, their search engine is shamefully bad. It’s embarrassingly, frustratingly, painfully bad. (…)

… I can hold a paper in my hands, search for two authors’ last names and have PubMed come up with nothing. (….)

Why is PubMed so behind the times? Why? How does it even work? Does it search only the abstract? Does it also search the body of the papers that are available online? Why does it get so massively confused by an author’s initials and last name together, in one search. [...]

I don’t think I should have to be, or enlist the services of, a medical librarian in order to do a simple search on a literature search engine. PubMed should be an intuitive search engine such as Google, or others. [...] PubMed should be tuned to my needs and my skill set. I should not have to tune to it. [...]“

There was an overwhelming response to her post and Anna’s story was covered in many blogs. I don’t want to revive that discussion, just want to mention Graham Steele’s comment.

“@ Anna,

You might just be in luck thanks to voicing your frustrations online !!

I brought this post to the attention of Dr Lipman who I’ve just heard back from.

He’s authorized me to post here on his behalf. (Thanks Dr Lipman)

Although the current engine works well for some users and some queries, I understand Anna’s frustration and we are in the midst of a number of changes that will make PubMed work better for her and many other users.

We will be adding a number of other “sensors” which will run in parallel with the default search. From monitoring results of enhancements we’ve added to some of our other Entrez databases.

A number of these complaints are fair and we’ll be doing our best to address them. With the large number of users we have, it will be clear what areas we’ll improving and what areas will need more work.”

I’m now beginning to understand what Graham Steel meant in his reply to Anna.

Coincidantly or not, PubMed has introduced a couple of changes that seem to concede Anna’s demands. This will be the subject of the second part of this Trilogy, see HERE

—————-

NL flag NL vlag

I.The Past:Extremely simple, yet incredibly difficult

Zoeken in PubMed is nooit makkelijk geweest, voor wie dan ook, beginner of gevorderde.

Als je echt volop gebruik wil maken van PubMed dan moet je niet alleen overweg kunnen met de zoekbalk, maar ook met de MeSH database. Je moet weten wat bredere en nauwere termen zijn, weten wanneer automatische explosie gewenst is of niet, wanneer je major topics gebruikt, subheading toevoegt en of je MeSH-termen via ‘Links’ of via de ‘Search to Sendbox’ naar PubMed ‘brengt’. Je moet weten of en hoe je Clinical Queries, Limits, Field Codes (tags), de History, MyNCBI saved searches and collections, linkouts, AND, OR, NOT enzovoorts, enzoverder gebruikt….

Het duurt dus even voor je alle ins en outs kent en op een effectieve manier van de geavanceerde mogelijkheden van PubMed gebruik maakt.

Voor de minder gevorderde gebruikers of de mensen die snel een antwoord willen op een (bio)medische vraag zoals artsen in de drukke klinische praktijk, fundamentele wetenschappers, preklinici voldeed vaak de zoekbalk. Je kon hier gewoon wat woorden intypen en ongezien zoekt (zocht) PubMed niet alleen in titel en abstract, maar vertaalde ze woorden ook in MeSH (als ze als synoniem herkend worden). Dit heet (automatic term) mapping of ATM. Makkelijk, maar het is wel aan te bevelen de “Details”-tab te bekijken om te zien of de search goed vertaald wordt. Soms gaat het namelijk helemaal fout. Bijv. als je walking aids typt, wordt o.a. op de MeSH voor de ziekte Aids gezocht, terwijl dat er natuurlijk niets mee van doen heeft.

Om de enorme hoeveelheid hits te reduceren kun je Limits of Methodologische Filters in de Clinical Queries (EBM-vragen) toepassen. Omdat de MeSH nogal georienteerd zijn op ziekten, is PubMed niet bij uitstek geschikt voor niet-medische vragen. Dit kan nog wel eens tot frustaties leiden. (zie onder)

Wanneer je alleen maar bepaalde artikelen wil opzoeken, kun je dat heel handig doen via de Single Citation Mapper. Typ gewoon de naam van een auteur, het tijdschrift, het pagina- of volumenummer, en/of een titelwoord in. En het artikel is zo gevonden.

Bij het opsommen van al deze mogelijkheden gaat het me al duizelen. Hoe moet het dan op beginners overkomen?

Na een PubMedcursus verzuchtte een student met veel ervaring in programmeren tegen mij.

“Wat een mogelijkheden, maar het is wel heel erg verborgen allemaal en erg moeilijk te vinden. Niet erg gebruikersvriendelijk.

Dat is zondermeer waar en omdat de PubMed zoekbalk oppervlakkig gezien wel op Google lijkt gaan onervaren zoekers (en met name de Google-generatie) erin zoeken als in Google. Ze typen de hele zoekstrategie gewoon in en verwachten dan snel wat te vinden. Helaas is dat niet zo. Zeker specifieke artikelen kon men zo vaak juist niet vinden, omdat wel automatisch met MeSH gemapt werd, maar meestal (juist niet) in het tijdschrift- of auteursveld gezocht werd. Daar was nu juist die handige Single Citation Mapper voor. Veel mensen kennen die echter niet, want de naam is nietszeggend en de optie zit in de blauwe zijbalk verscholen.

Ook promovenda Anna Kushnir liep hier tegenop en blies daarover stoom af op haar blog:

“I hate PubMed. I hate it with a burning passion. For a site that is as vital to scientific progress as PubMed is, their search engine is shamefully bad. It’s embarrassingly, frustratingly, painfully bad. (…)

… I can hold a paper in my hands, search for two authors’ last names and have PubMed come up with nothing. (….)

Why is PubMed so behind the times? Why? How does it even work? Does it search only the abstract? Does it also search the body of the papers that are available online? Why does it get so massively confused by an author’s initials and last name together, in one search. [...]

I don’t think I should have to be, or enlist the services of, a medical librarian in order to do a simple search on a literature search engine. PubMed should be an intuitive search engine such as Google, or others. [...] PubMed should be tuned to my needs and my skill set. I should not have to tune to it. [...]“

Dit blog heeft heel wat losgemaakt, zowel onder voor- en tegenstanders. Ik zal nu niet het stof weer doen opwaaien, maar ik wil alleen nog even Graham Steele’s commentaar vermelden.

@ Anna,

You might just be in luck thanks to voicing your frustrations online !!

I brought this post to the attention of Dr Lipman who I’ve just heard back from.

He’s authorized me to post here on his behalf. (Thanks Dr Lipman)

Although the current engine works well for some users and some queries, I understand Anna’s frustration and we are in the midst of a number of changes that will make PubMed work better for her and many other users.

We will be adding a number of other “sensors” which will run in parallel with the default search. From monitoring results of enhancements we’ve added to some of our other Entrez databases.

A number of these complaints are fair and we’ll be doing our best to address them. With the large number of users we have, it will be clear what areas we’ll improving and what areas will need more work.

Ik begin nu een beetje te begrijpen wat Graham hiermee bedoelde.

Want toevalligerwijs of niet, zijn er enkele zaken ingrijpend veranderd in PubMed, veranderingen die Anna’s eisen lijken in te willigen.

Welke veranderingen dat zijn en wat voor een effect ze sorteren wordt in deel 2 van deze trilogie besproken, zie HIER

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6 responses

11 06 2008
Database Management » Blog Archive » PubMed: Past, Present And Future, PART I

[...] Blog wrote an interesting post today onHere’s a quick excerpt I.The Past: Extremely simple, yet incredibly difficult Searching PubMed has never been easy, not for the advanced searcher nor the beginner. As an advanced searcher you have (had?) to find your way through the Search Bar, MeSH-database, look for broader, narrower or related terms, know when to explode MeSH, add major topics or subheadings or not, know when to use ‘Links’ or the ‘Search to Sendbox’ to send Searches to PubMed. Know when and how to use Clinical Queries, Limits, Field Codes ( [...]

17 06 2008
Medicine 2.0: The show goes on « ScienceRoll

[...] great posts about the past, present and future of Pubmed, the search engine of health science data (part I and part [...]

17 06 2008
Pack of Sensations » Blog Archive » Medicine 2.0: The show goes on

[...] great posts about the past, present and future of Pubmed, the search engine of health science data (part I and part [...]

8 07 2008
Anthony

Have you tried “CureHunter.com“? They have a really interesting relational approach to mapping and searching Pubmed. They are focused on finding the best treatment options for disease, but it looks like you could search for any molecular compound.

4 08 2008
Pubmed: past, present and future : Physio 2.0

[...] past, present and future I came across this article discussing the past, present and future of the Pubmed database. I was browsing through the Medicine [...]

1 04 2009
PubMed Changes at the Front Door « Laika’s MedLibLog

[...] Pubmed: past present and future – part-i/ the past(2008/06/11/) [...]

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