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Faire sa biblio dans #PubMed sans s'arracher les cheveux: un (long) thread

⚠️ Précaution d'emploi (1/2)

Les trucs et astuces qui suivent ne sont valables que pour une utilisation « au quotidien » de PubMed. N'utilisez pas les outils qui suivent pour réaliser une revue systématique ou une méta-analyse !!!!
⚠️ Précaution d'emploi (2/2)

Tout ceci est destiné à faire des recherches rapides, sans se prendre la tête et sans y passer des heures.

Ca ne remplace *évidemment pas* l'aide que peut vous apporter un(e) documentaliste en santé pour des recherches plus fines. 🤓
Read 102 tweets
A #thread on our recent paper in @PLOSNTDs examining ecological #evidence-base for #DiseaseControl management practices for #KyasanurForestDisease #AcademicTwitter #Scicomm #OneHealth; paper led by @SarahBurthe from @MonkeyFever_ consortium
#Diseasecontrol strategies originate through endorsements by Governments/academia/authorities; they're often not field-tested robustly; even when they are, evidence is limited to one sector (cf. #OneHealth #Intersectoral approaches);
#publichealth approaches ought to be contextual & their effectiveness ought to be evaluated, yet strategies for disease control often spread through word of mouth and are sometimes untested;
Read 50 tweets
What happens to hematopoietic transplant recipients who develop #COVID19?

Transplant recipients and transplanters have been asking this question ever since the pandemic began.

Our analysis using @CIBMTR data is out today in @TheLancetHaem…. 1/
While there have been close to 100,000 papers related to COVID-19 listed on @NCBI @NLM_NIH #Pubmed, there are very few that address outcomes after #COVID19 in #BMTsm patients, a few are listed in the next tweet: 2/
Read 19 tweets
Happy Wednesday! Join me, won't you, for another #medlibs rant thread / tweetorial in which I discuss the age group filters in #PubMed. I'm going to use the search

[ cyclic vomiting[tw] ]

as my example. You have been warned. 😅 screenshot to show the age filters in PubMedscreenshot of age filters in PubMed where you can select to
My question that I referenced in this tweet was asking about what is really happening with these filters. I eventually got an answer, but I had to do the work myself to really get it. Sharing here with y'all since it's not documented elsewhere.

A few caveats: these age filters are all based on Medical Subject Headings, or MeSH terms, which immediately restricts their usefulness since not everything in PubMed is indexed with MeSH. That's not to say they are 'bad' though - they can be very helpful. For example:
Read 32 tweets
Separating the #men from the #boys
Here is a #PubMed #indexed, #Elsevier published #journal reporting '#exclusive' #treatment of #covid19 through #Ayurveda leading to full recovery in a #patient. Great #news right?! No. The #proof of the #pudding is in the eating! Spoons out
The #journal. Its legit, 'becoz' its publishd by #Elsevier. Journal ownd by World Ayurveda Foundation & Trans-Disciplinary Univ, #Bengaluru. 4mer, a 4-men 'world foundation'[], latter @TDUFRLHT founded @sampitroda, vettedby likes of @kiranshaw
The study - 43yr old #newyork #banker develops fever,cough durng peak #COVID season, 'PRESUMED' to be #coronavirus. Self #Quarantine at #home, phone calls #ayurvedic #Doctors at #Chennai, #india, offer☎️ treatmnt until fever break, therby reporting #covid19 cure via Ayurveda
Read 13 tweets
🔥J'avais promis un thread sur ma présentation orale au congrès européen sur #COVID19 #ECCVID @ESCMID :
#Hydroxychloroquine: pros and cons
Congrès qui remplace @ECCMID annulé cette année

1/n Image
Le début de ce délire collectif autour #hydroxychloroquine peut être tracé au 25/02/2020 lorsqu'un microbiologiste français affirma
"une amélioration spectaculaire" ac #HCQ l''infection pulmonaire la plus facile à traiter" et a conseillé de courir en cherchesr d les pharmacies Image
Le 25/02/20, déjà impliqué dans la recherche thérapeutique #COVID19 je me souviens avoir couru sur #PubMed @NCBI chercher les données cliniques que j'avais manquées et qui permettait d'affirmer cela.
La recherche fut rapide : Image
Read 34 tweets
¿Conoces la historia de PubMed? Seguro que buscas en el asiduamente, pero sabes de dónde viene?
En este hilo te lo cuento 1/11
PubMed permite el acceso gratuito X Internet desde 01/1996 a la base de datos MEDLINE. Y siendo verdad también hay que señalar que PubMed no solo es MEDLINE aunque su mayor componente sea este. Más información ¿Pero no es lo mismo PubMed que MEDLINE? 2/11…
El antecedente de MEDLINE es el Index Medicus (1879 x John Shaw Billings, mensual). Una versión acumulada anual (CUMULATED INDEX MEDICUS) 1960-2004. Una versión reducida 1970-1997 (ABRIGDE INDEX MEDICUS) con la indización de revistas nucleares.
Hilo 3/11…
Read 13 tweets
Cómo funciona el nuevo PubMed: ¿Por qué da resultados diferentes el Legacy vs. nuevo PubMed?…
Los motivos de por qué da diferentes resultados el antiguo del nuevo PubMed son tres…
Nuevo vs. Legacy #PubMed PubMed: son 2 sistemas independientes en los que la indexación se realiza en diferentes momentos, por lo que las adiciones, eliminaciones (por ejemplo, eliminar duplicados) o actualizaciones de registros no surten efecto al mismo tiempo en ambos lugares.
Read 6 tweets
La dizione #Asintomatico compare più spesso in pubblicazioni scientifiche con (o senza ma con evidente riferimento a) varia ulteriore #specificazione e rivolto a soggetti #affetti (es. infezioni: #asintomatici #infetti, pazienti infetti asintomatici, casi asintomatici, ecc.) 1/14
ma #senza #manifestazioni cliniche (sintomi e segni). Tuttavia pare che il termine #asintomatico abbia anche un significato più ampio, cioè di soggetto #senza #manifestazioni cliniche il cui esatto #stato di #salute, di #affetto o meno, sia #determinabile solo con un #test. 2/14
Almeno così potrebbe sembrare dalle letture di un profano come me che ha fatto alcune ricerche. Ad es. su #PubMed sono molteplici le pubblicazioni che esplicitano che gli #asintomatici possano essere anche #non #infetti e #negativi alla diagnostica. 3/14
Read 15 tweets
My team and I are seeing a big spike in requests from people looking for #COVID_19 related related. The good news is that there are already a bunch of efforts to highlight, curate, and make this work available.

Here's some (and feel to suggest others)!
COVID-19 Open Research Dataset (CORD-19)

Put together by @allen_ai, @czi, @CSETGeorgetown, @microsoft, and @nlm_news.

Machine-readable collection of articles in PMC, preprints in @biorxivpreprint/@MedArXiv, metadata from articles published elsewhere.…

From @nlm_news.

Links to relevant articles in #PubMed. Updated daily and broken down by topic and geographic location.…
Read 9 tweets
OJO a las bibliotecas que todavía usan LinkOut utilizando Outside Tool en #PubMed (HILO) Image
As of February 28, 2020, LinkOut via Submission Utility and LinkOut Local services will be discontinued. Library icons will continue to display in legacy #PubMed PubMed, but holdings data will not be updated after February 28, 2020.
Libraries that participate in Library LinkOut using Outside Tool can activate their library icon in the new #PubMed PubMed using the URL where nameabbr
NLM Technical Bulletin. 2019 Nov–Dec
Read 3 tweets
Una cosa sobre el Nuevo #PubMed Tienen un botoncito de feedback para decirles cosas. Yo les digo cosas como que necesito el enlace a MeSH para hacer las búsquedas. Me responden cosas como: "We suggest entering search terms without search tags for the most comprehensive retrieval"
It's a trap! ¿Por qué? Porque os va a hacer la búsqueda de los términos en TODOS los campos. He hecho la prueba y he metido una frase tal cual, sin las comillas y sin etiquetas de campo. Y el resultado ha sido un desastre: sólo un registro.
La cosa cambia si pones esa misma frase entrecomillada o si le indicas dónde quieres que busque. Porque por mucho que se empeñen, su niño no es el más listo. La utopía de buscar tipo Google en PubMed está muy bien, pero PubMed no es Google.
Read 10 tweets
There may be variations in your search results due to enhanced synonymy, addition of plural forms, better British/American translations, unlimited truncation, and slight differences in how the new system indexes words and phrases.
I have performed the following search: pregnancy [ti]
In old PubMed the result is 167194 references and in the new #PubMed search engine 167213 references.
I know that the search algorithm has changed but the search by tags should be the same result.
Response of NLM: "individual search field results may be slightly increased using the updated technology as it is more robust in ignoring special characters associated with citation content".
Read 3 tweets
The New #PubMed is Here. The new PubMed will become the default in spring 2020 and will ultimately replace the legacy version. NLM Technical Bulletin. 2019 Nov–Dec… Image
In the new #PubMed search details (including mapping to MeSH and additional synonyms) are in the Advanced search page. To modify the details, copy and paste the text to the search box and edit.
RSS feeds are not currently supported in the new #PubMed system. Send your suggestions using the Feedback button on the PubMed Labs pages.
Read 5 tweets
Webinar el 25 de septiembre del nuevo My Bibliography (funcionalidad para salvar y compartir nuestras referencias) de #PubMed: An insider's guide to the new My Bibliography… vía @NCBI
Read 3 tweets
Since a few #medlibs asked... I've dug up some of my favorite examples of bad / wtf MeSH indexing, along with a few of my go-to searches to show how automatic term mapping (ATM) in #PubMed can do unexpected things.

A thread 👇
"The importance of good images in using hair to screen for breast cancer" ( has been indexed with "Magic"[Mesh]. I'm guessing it's because the next letter, on page 2 of pdf, has the title "Science or Black Magic?" #medlibs…
I mentioned this one during the #medlibs chat:

MeSH fun includes being indexed with "Telepathy"[Majr]. I assume based on context it should maybe have been "Telepathology"[Mesh]. But also... did you know there is a Mesh term for telepathy?
Read 12 tweets

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