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 ...
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/
On Friday, July 25th, starting at 9:00 PM EDT, we’ll be performing essential maintenance on the NLM data center. This upgrade is critical to ensure the continued reliability and stability of our services. We anticipate this planned outage will last 24 hours or more. During this time, users may experience interrupted access or degraded performance … Continue reading NCBI Website Maintenance — Beginning July 25th →
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!
https://ncbiinsights.ncbi.nlm.nih.gov/2025/07/08/ncbi-website-maintenance-july-26th/
On Friday, July 25th, starting at 9:00 PM EDT, we’ll be performing essential maintenance on the NLM data center. This upgrade is critical to ensure the continued reliability and stability of our services. We anticipate this planned outage will last 24 hours or more. During this time, users may experience interrupted access or degraded performance … Continue reading NCBI Website Maintenance — Beginning July 25th →
PubMed Update: FTP Improvements Available for Testing https://www.nlm.nih.gov/pubs/techbull/mj25/mj25_pubmed_ftp_data.html
The National Library of Medicine (NLM) is committed to advancing biomedical discovery across our databases of biomedical literature, genomic information, and other scientific data. As part of these efforts, NLM strives to produce timely MeSH indexing of MEDLINE biomedical and life sciences citations for the PubMed database. To this end, the Library is pleased to announce the next major milestone in automated MEDLINE indexing: the implementation of the MTIX (Medical Text Indexer-NeXt Generation) algorithm, which replaces the MTIA (Medical Text Indexer-Automated) algorithm. MTIX Technology Although MTIA and MTIX have similar names, they use different technologies. MTIA was a complex system based on a dictionary of MeSH terms, synonyms, and other trigger phrases, with rules created and refined by humans over the course of many years. In contrast, MTIX is a machine learning model known as a neural network, a type of AI.MTIX was trained on millions of MEDLINE...
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
André Ourednik
Christian Meesters
Scott Cain
genehack
naturepoker
Pierre Lindenbaum
Walled Culture
Jorge
Darren
Thomas Sandmann