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Thomas SandmannBig 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 <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a> heroes doing priceless and highly impactful work! 🦸 🧬 💻 <a href="https://genomic.social/tags/NCBI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NCBI</a> <a href="https://genomic.social/tags/nih" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#nih</a>

Victoria Stuart 🇨🇦 🏳️‍⚧️‘Omg, did PubMed go dark?’ Blackout stokes fears about database’s future <a href="https://www.nature.com/articles/d41586-025-00674-3" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.nature.com/articles/d41586-025-00674-3</a>A brief outage has focused attention on scientists’ reliance on the US-government-funded website.Comment: a fundamental and vitally important biomedical resource, the importance of which cannot be understated.<a href="https://mastodon.social/tags/PubMed" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#PubMed</a> <a href="https://mastodon.social/tags/PubMedCentral" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#PubMedCentral</a> <a href="https://mastodon.social/tags/PM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#PM</a> <a href="https://mastodon.social/tags/PMC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#PMC</a> <a href="https://mastodon.social/tags/biomedical" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#biomedical</a> <a href="https://mastodon.social/tags/BiomedicalLiterature" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#BiomedicalLiterature</a> <a href="https://mastodon.social/tags/NLM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NLM</a> <a href="https://mastodon.social/tags/NCBI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NCBI</a>

Noam RossRegarding <a class="hashtag" href="https://bsky.app/search?q=%23NIH" rel="nofollow noopener noreferrer" target="_blank">#NIH</a> websites, including <a class="hashtag" href="https://bsky.app/search?q=%23RePORTER" rel="nofollow noopener noreferrer" target="_blank">#RePORTER</a>, <a class="hashtag" href="https://bsky.app/search?q=%23PubMed" rel="nofollow noopener noreferrer" target="_blank">#PubMed</a>, <a class="hashtag" href="https://bsky.app/search?q=%23NCBI" rel="nofollow noopener noreferrer" target="_blank">#NCBI</a>, 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:

tyxNew shitty reality: Every time <a href="https://lor.sh/tags/NCBI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NCBI</a> is <a href="https://lor.sh/tags/down" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#down</a> you wonder whether it's permanent or not.Just now the whole nih.gov is not resolving from two different locations I have access to. Also: <a href="https://downdetector.com/status/nih/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://downdetector.com/status/nih/</a>And just in time when I decided to do some <a href="https://lor.sh/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a> work 1AM on Sat^W Sunday.<a href="https://lor.sh/tags/nih" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#nih</a>

Björn BrembsI have an idea how the <a href="https://mastodon.social/tags/NIH" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NIH</a> could increase their efficiency and make Trump very happy 😇 How about the NIH decentralizes all <a href="https://mastodon.social/tags/PUBMED" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#PUBMED</a> <a href="https://mastodon.social/tags/NCBI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NCBI</a> <a href="https://mastodon.social/tags/NLM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NLM</a> 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?<a href="https://mastodon.social/tags/library" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#library</a> <a href="https://mastodon.social/tags/medicine" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#medicine</a> <a href="https://mastodon.social/tags/research" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#research</a> <a href="https://mastodon.social/tags/science" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#science</a>

Luke PembletonSo with Trump likely to shake up NIH, do we need to be worried about <a href="https://genomic.social/tags/NCBI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NCBI</a> 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.<a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a> <a href="https://genomic.social/tags/genomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#genomics</a> <a href="https://genomic.social/tags/biotechnology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#biotechnology</a>

Bioinfo-fr.net📰 Aujourd'hui, on vous racconte comment soumettre des données de séquençage à la plateforme GEO : <a href="https://bioinfo-fr.net/chronique-dune-soumission-de-donnees-a-geo" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://bioinfo-fr.net/chronique-dune-soumission-de-donnees-a-geo</a> <a href="https://mamot.fr/tags/bioinfofr" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinfofr</a> <a href="https://mamot.fr/tags/data" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#data</a> <a href="https://mamot.fr/tags/ngs" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ngs</a> <a href="https://mamot.fr/tags/ncbi" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ncbi</a>

ℵ₀ 🏳️‍⚧️🏴‍☠️<a href="https://ncbiinsights.ncbi.nlm.nih.gov/2017/06/22/pubmed-available-for-download-without-license/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://ncbiinsights.ncbi.nlm.nih.gov/2017/06/22/pubmed-available-for-download-without-license/</a>Just a reminder.<a href="https://mastodon.social/tags/PUBMED" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#PUBMED</a> <a href="https://mastodon.social/tags/NCBI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NCBI</a> <a href="https://mastodon.social/tags/NLM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NLM</a> <a href="https://mastodon.social/tags/library" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#library</a> <a href="https://mastodon.social/tags/medicine" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#medicine</a> <a href="https://mastodon.social/tags/research" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#research</a> <a href="https://mastodon.social/tags/science" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#science</a> <a href="https://mastodon.social/tags/fightcensorship" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#fightcensorship</a>

GBIF 🌱Are you sitting on microbiome data collected in <a href="https://ecoevo.social/tags/Africa" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Africa</a>?🔍 Join <a href="https://ecoevo.social/tags/MiCoDa" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#MiCoDa</a> from 6-8 Nov for the <a href="https://ecoevo.social/tags/DatathonAfrica" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#DatathonAfrica</a> - 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 <a href="https://ecoevo.social/tags/NCBI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NCBI</a> formats and collaborate with experts. More info: 🔗 <a href="https://buff.ly/3BJ4tCQ" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://buff.ly/3BJ4tCQ</a>

Tom Madden<a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/07/18/new-blast-core-nucleotide-database/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://ncbiinsights.ncbi.nlm.nih.gov/2024/07/18/new-blast-core-nucleotide-database/</a><a href="https://mastodon.social/tags/NCBI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NCBI</a> <a href="https://mastodon.social/tags/UseBLAST" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#UseBLAST</a> <a href="https://mastodon.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Bioinformatics</a>

DarrenYou have to love the <a href="https://sfba.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a> field. I'm dealing with a data set from <a href="https://sfba.social/tags/ncbi" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ncbi</a> 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..

Dong-Ha OhCGV paper is out. Alignments are added per request, and I guess the team would love to hear any user feedback. :) <a href="https://genomic.social/tags/comparativegenomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#comparativegenomics</a> <a href="https://genomic.social/tags/NCBI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NCBI</a> <a href="https://doi.org/10.1371/journal.pbio.3002405" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://doi.org/10.1371/journal.pbio.3002405</a>

Peter CockLearnt a new trick with <a href="https://fediscience.org/tags/NCBI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NCBI</a> <a href="https://fediscience.org/tags/EntrezDirect" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#EntrezDirect</a> tools:$ xtract -pattern ENTREZ_DIRECT -element Count < search.xmlMore 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.

Spaceflight 🚀<a href="https://spacey.space/tags/NCBI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NCBI</a> 📆 2020 <a href="https://spacey.space/tags/Solar" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Solar</a> Minimum will lead to terrestrial cooling ❄️. In the next 500 years there are two modern grand solar minima approaching in the <a href="https://spacey.space/tags/Sun" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Sun</a> ☀️, the modern one in the 21st century (📆 2020–2053). The reduction 📉 of <a href="https://spacey.space/tags/terrestrial" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#terrestrial</a> temperature during the next 30 years can have important implications for different parts of the planet on growing vegetation, agriculture 🌾, food supplies 🍽️, and heating 🌡️ needs <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7575229/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7575229/</a><a href="https://spacey.space/tags/SpaceWeather" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SpaceWeather</a> <a href="https://spacey.space/tags/ClimateChange" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ClimateChange</a> <a href="https://spacey.space/tags/NationalLibraryOfMedicine" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NationalLibraryOfMedicine</a>

Thomas Sandmann<a href="https://mastodon.social/@gvwilson" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@gvwilson</a> Perhaps the NCBI dataset API could be useful? You can e.g. enter Entrez gene identifiers and get information about gene identifiers & synonyms: <a href="https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/rest-api/#get-/gene/id/-gene_ids-" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/rest-api/#get-/gene/id/-gene_ids-</a> The output is well structured, but there are fields of varying lengths for different genes (because they have different numbers of synonyms, database ids, etc).Here is an example query for gene (entrezid) 59067: <a href="https://api.ncbi.nlm.nih.gov/datasets/v2alpha/gene/id/59067?table_fields=gene-id&table_fields=gene-type&table_fields=description" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://api.ncbi.nlm.nih.gov/datasets/v2alpha/gene/id/59067?table_fields=gene-id&table_fields=gene-type&table_fields=description</a> Switch out 59067 for another entrez identifier to get more examples. <a href="https://genomic.social/tags/NCBI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NCBI</a> <a href="https://genomic.social/tags/REST" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#REST</a> <a href="https://genomic.social/tags/JSON" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#JSON</a>

Teresita Porter 🙋🏻‍♀️Database resources of the National Center for Biotechnology Information<a href="https://doi.org/10.1093/nar/gkad1044" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://doi.org/10.1093/nar/gkad1044</a><a href="https://ecoevo.social/tags/ReferenceSequence" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ReferenceSequence</a> <a href="https://ecoevo.social/tags/Databases" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Databases</a> <a href="https://ecoevo.social/tags/NCBI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NCBI</a> <a href="https://ecoevo.social/tags/GenBank" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#GenBank</a> <a href="https://ecoevo.social/tags/PubMed" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#PubMed</a> <a href="https://ecoevo.social/tags/SRA" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SRA</a> <a href="https://ecoevo.social/tags/RefSeq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RefSeq</a> <a href="https://ecoevo.social/tags/Taxonomy" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Taxonomy</a> <a href="https://ecoevo.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a>

Dong-Ha OhGene Ontology is being added for all NCBI RefSeq Eukaryote genomes (1.7K and growing), called by interProScan + Panther/TreeGrafter :) <a href="https://genomic.social/tags/NCBI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NCBI</a> <a href="https://genomic.social/tags/GeneOntology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#GeneOntology</a> <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2023/11/15/gene-ontology-terms-refseq-eukaryotic-genomes/?utm_source=ncbi_twitter&utm_medium=referral&utm_campaign=refseq-go-terms-20231115" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://ncbiinsights.ncbi.nlm.nih.gov/2023/11/15/gene-ontology-terms-refseq-eukaryotic-genomes/?utm_source=ncbi_twitter&utm_medium=referral&utm_campaign=refseq-go-terms-20231115</a>

Dong-Ha OhA bit more detailed on how to navigate genome alignments on CGV or the Comparative Genome Viewer (and you can request to add alignments for any pairs of chromosome-level assemblies if they are on NCBI) (and they are not too far apart) (and with similar ploidy levels, for now) :) <a href="https://genomic.social/tags/comparativegenomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#comparativegenomics</a> <a href="https://genomic.social/tags/NCBI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NCBI</a> <a href="https://youtu.be/_TA86Tu1N0c" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://youtu.be/_TA86Tu1N0c</a>

Dong-Ha OhComparative Genomics Viewer by <a href="https://genomic.social/tags/NCBI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NCBI</a> - the browsing experience is quite cool, and I guess more species pairs will be added (they are accepting requests) :) <a href="https://genomic.social/tags/comparativegenomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#comparativegenomics</a> <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2023/02/22/cross-species-cgv/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://ncbiinsights.ncbi.nlm.nih.gov/2023/02/22/cross-species-cgv/</a>

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