#ncbi — Public Fediverse posts

L’arbre miracle : Moringa oleifera, une plante originaire de l’Inde et du Pakistan
Photo prise au Jardin botanique de Montréal
http://monde.ccdmd.qc.ca/ressource/?id=119999
Documentation scientifique :
https://pmc.ncbi.nlm.nih.gov/articles/PMC9916933/
#plante #botanique #science #médicament #remède #Inde #Pakistan #jardin #Montréal #pmc #ncbi #nlm #nil #recherche #photo #photographie #photography

a constant thorn in my side is the shambles that "reference" genomes and annotations are often in, when you take a closer look.

the #NCBI RefSeq annotation for zea mays has literal sequence identity for the 18S subunit in both the chloroplast and the mitochondrial genomes (probably an assembly error). It also lists identical subunits in the chloroplast: one called "4.5" and the other "4.5S", just in case you were hoping for a consistent naming scheme. FML!!!!

https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_902167145.1/

Today's job required colecting and combining info from @[email protected], #KEGG and #NCBI. Integrating with #bioinformatics tools in #Rstats and @[email protected] These biological data resources and tools must surely be amongst the greatest achievements of modern science.

Happy New Year to all of you!
I hope this year will bring us better relationships with all living beings than the last one.

To contribute to these, I propose the project #OuroborosTree :

https://ourednik.info/OuroborosTree

Database and visual application for exploring relations between human #nutrition and living organisms.

It harmonizes data from #NCBI, #FAO, #OSAV, #Wikimedia and #iNaturalist.

Contact me for collaboration on further development or integration of OuroborosTree in your project.

Just did some queries using NCBI's `dataset` utility program.

It only worked 1 time in a dozen or so trials.

If NCBI is getting instable, for whatever reason, is there an EU alternative?

The commands were like

`datasets download genome accession {params.accession} --include genome`

So, even if there is a mirror, software support is another issue to solve ...

#NCBI #RDM #unplugTrump

Let me start with: I don’t really know. That said, I think community aspects are taken into account but also, #NCBI is (I think) purposely conservative and won’t change too quickly. I imagine it is in their queue to evaluate the new assembly to make it the reference but yeah, it takes time
@lwpembleton

Since the current …everything has folks a little on edge about .gov websites going down, be aware that #NCBI (hosts of #Pubmed, #GenBank, and other important #biomed database sites) will be offline from this Friday evening into the weekend.

(Consider re-sharing if you have an audience that would appreciate knowing.)

https://ncbiinsights.ncbi.nlm.nih.gov/2025/07/08/ncbi-website-maintenance-july-26th/

NLM will be going through a major server maintenance from July 25th to July 28th. I'd say avoid NCBI upload/usage during that time!

#bioinformatics #NCBI

https://ncbiinsights.ncbi.nlm.nih.gov/2025/07/08/ncbi-website-maintenance-july-26th/

PubMed Update: FTP Improvements Available for Testing https://www.nlm.nih.gov/pubs/techbull/mj25/mj25_pubmed_ftp_data.html

#pubmed #ncbi #bioinformatics

Trump’s war on knowledge requires re-inventing academic publishing as diamond open access

A year ago, Walled Culture wrote about a growing risk that we will lose access to the world’s knowledge, because of a failure by traditional academic publishers to place copies of the articles they publish in key backup archives. Although unacceptable, that oversight is more a matter of laziness and cost cutting on the part of publishers, rather than a result of outright animosity to the […]

#academicPublishing #archives #climateCrisis #diamondOa #donaldTrump #fair #nasa #ncbi #nih #noaa #nsf #pangaea #pubmed #samizdat #zbMed

https://walledculture.org/trumps-war-on-knowledge-requires-re-inventing-academic-publishing-as-diamond-open-access/

Lights barely still on over at the #NIH. #ncbi Clicked on the search link for #GEO just now and got this

Big shoutout to the folks at NCBI GEO. They have been doing an incredible job managing enormous amounts of gene expression and related biomedical data for many, many years They do it efficiently and very, very well. I am so grateful: both when I download data published by others and when I submit my own data. You are true #bioinformatics heroes doing priceless and highly impactful work! 🦸 🧬 💻 #NCBI #nih

Regarding #NIH websites, including #RePORTER, #PubMed, #NCBI, being down: - This appears to be due to an issue with domain-name lookup. The websites are up, the lookup is (partially) broken - It could be caused by a denial-of-service attack or a misonfiguration 🧵 with explanation and workaround:

I have an idea how the #NIH could increase their efficiency and make Trump very happy 😇

How about the NIH decentralizes all #PUBMED #NCBI #NLM etc. databases with EBI and other similar institutes around the world, so that the US isn't the only country having to pay for these services? Wouldn't Trump just love to see the other countries paying their fair share as well? 😆

This day and age, it should be an easy sell?

#library #medicine #research #science

So with Trump likely to shake up NIH, do we need to be worried about #NCBI and access to all the sequence data and genomes? Downloading a local copy of Wikipedia is one thing, but downloading NCBI is just not practical...

I know a lot of groups, particularly those funded primarily by grants, upload all their genomic data to NCBI at the end of a project because they cannot afford to retain local copies indefinitely.

#bioinformatics #genomics #biotechnology

📰 Aujourd'hui, on vous racconte comment soumettre des données de séquençage à la plateforme GEO :
https://bioinfo-fr.net/chronique-dune-soumission-de-donnees-a-geo
#bioinfofr #data #ngs #ncbi

@Linux
@Linux_Is_Best

Here PEER REVIEWED!

### Are Parenting Practices Associated with the Development of #Narcissism ? Findings from a Longitudinal Study of Mexican-origin Youth - #PMC

> Our study showed that parental hostility and parental monitoring were related to adolescents’ exploitativeness two years later, indicating that parenting practices play a central role in the development of narcissism during adolescence.

https://pmc.ncbi.nlm.nih.gov/articles/PMC5193228/

#NCBI

Are you sitting on microbiome data collected in #Africa?🔍

Join #MiCoDa from 6-8 Nov for the #DatathonAfrica - a virtual event that aims to increase the discoverability and reusability of regional microbial data! 📊

🧬 Hear from researchers about the reuse of biodiversity data. upskill on formatting your metabarcoding sequence data for #NCBI formats and collaborate with experts.

More info: 🔗 https://buff.ly/3BJ4tCQ

Big update to #PubMedCentral (PMC) website at #ncbi! You’ll notice a new look, feel, and organization of PMC article pages and the PMC Journal List. Learn more: https://ow.ly/um7C50TPOOB

Just filled in the #NCBI #Blast 2024 survey https://nlmenterprise.co1.qualtrics.com/jfe/form/SV_06P1niEO0KxXJGe and struggled briefly on the wish list box - then brought an old idea to mind:

A new TSV output like format 6 but with a one line header consisting of the column names (as per the command line terms) tab separated with a leading "'#". This would allow easy parsing into data frames with labelled columns, and also distinguish between no hits (which would still have a header line) and an empty file due to failed run.

Anyone knows where can I find a list of valid types for "Dataset Type" when searching for NCBI GEO Datasets?

The help pages only mention "expression profiling by high throughput sequencing" as an example.

#bioinformatics #GEO #ncbi

NCBI will be phasing out their entrez tools this year, so testing out their new datasets tool as replacement.

So far it's been great. Essentially a more general purpose, officially NCBI backed version of the famous ncbi-genome-download package people are already familiar with.

A quick download of genome accession set is as simple as:

datasets download genome accession --inputfile tmp.acc

Which certainly beats my 31 line script calling on entrez

#bioinformatics #ncbi

You have to love the #bioinformatics field. I'm dealing with a data set from #ncbi right now where they have project ids, sample ids, run ids, experiment ids, GEO ids, sample names, study ids, platform ids and yet the authors still crammed the most useful piece of information (which patient matches which sample) with underscores into the title field. And every study does this differently..

Learnt a new trick with #NCBI #EntrezDirect tools:

$ xtract -pattern ENTREZ_DIRECT -element Count < search.xml

More elegant and readable than the grep I was using before.

For context, sadly I still sometimes get "silent" failures where efetch returns partial data and a return code of 0 ("success"). It does grumble on stderr.

Thus the need to compare the record count after efetch to the expected count from esearch.

Anyone else noticed https://ftp.ncbi.nih.gov/ doesn't resolve anymore (tried HTTPS, HTTP, FPT, Ping - not a protocol issue)? Worked on 7 March, broken on 8 March according to my CI logs. However, https://ftp.ncbi.nlm.nih.gov/ looks OK #NCBI