#ncbi — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #ncbi, aggregated by home.social.
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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.
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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.
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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.
-
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.
-
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.
-
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.
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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 ...
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https://www.europesays.com/ie/198966/ AlphaFold Database Structure Extractor: a web server and API to download AlphaFold structures using common protein accessions | BMC Bioinformatics #algorithms #AlphaFoldDB #APIToolkit #Bioinformatics #ComputationalBiology #ComputationalBiology/Bioinformatics #ComputerAppl.InLifeSciences #Éire #IE #Ireland #Microarrays #NCBI #OpenAccess #ProteinStructure #Science #StructuralGenomics #UniProt
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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/
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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/
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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/
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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/
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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/
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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/
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PubMed Update: FTP Improvements Available for Testing https://www.nlm.nih.gov/pubs/techbull/mj25/mj25_pubmed_ftp_data.html
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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
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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
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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?
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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?
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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?
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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?
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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?
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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.
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📰 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 -
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.
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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
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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
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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.
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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.
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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
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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..
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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.
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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
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#NCBI 📆 2020 #Solar Minimum will lead to terrestrial cooling ❄️. In the next 500 years there are two modern grand solar minima approaching in the #Sun ☀️, the modern one in the 21st century (📆 2020–2053). The reduction 📉 of #terrestrial 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 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7575229/
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@gvwilson Perhaps the NCBI dataset API could be useful? You can e.g. enter Entrez gene identifiers and get information about gene identifiers & synonyms: https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/rest-api/#get-/gene/id/-gene_ids- 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: https://api.ncbi.nlm.nih.gov/datasets/v2alpha/gene/id/59067?table_fields=gene-id&table_fields=gene-type&table_fields=description Switch out 59067 for another entrez identifier to get more examples. #NCBI #REST #JSON
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Now published: Mendes de Farias et al, Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giad058/7243539 #KnowledgeBase #bioinformatics #interoperability #FAIR @GigaScience @wikidata #NCBI #SIB #FAIRdata
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I learned recently that while the #EvoDevo and #phylogenomics literature overwhelmingly use the term #Metazoa, it is an obsolete junior synonym to #Animalia. #zoology
#NCBI taxonomy uses Metazoa, consistent with the use in molecular fields https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=33208&lvl=3&lin=f&keep=1&srchmode=1&unlock
but @gbif uses Animalia https://www.gbif.org/species/1, as does @Wikipedia https://en.wikipedia.org/wiki/Animal
As for #ICZN, they don't seem to care for modern concerns about phylogeny and such http://www.animalbase.uni-goettingen.de/zooweb/servlet/AnimalBase/loadcachedpage?url=animalbase-code.html -
More from our friends at #NCBI | Announcing the #GenBank and #SRA Data Processing Webpage | #OpenData #OpenScience | I like their documentation | https://ncbiinsights.ncbi.nlm.nih.gov/2023/01/10/genbank-sra-data-processing-webpage/
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More from our friends at #NCBI | Announcing the #GenBank and #SRA Data Processing Webpage | #OpenData #OpenScience | I like their documentation | https://ncbiinsights.ncbi.nlm.nih.gov/2023/01/10/genbank-sra-data-processing-webpage/
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More from our friends at #NCBI | Announcing the #GenBank and #SRA Data Processing Webpage | #OpenData #OpenScience | I like their documentation | https://ncbiinsights.ncbi.nlm.nih.gov/2023/01/10/genbank-sra-data-processing-webpage/
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More from our friends at #NCBI | Announcing the #GenBank and #SRA Data Processing Webpage | #OpenData #OpenScience | I like their documentation | https://ncbiinsights.ncbi.nlm.nih.gov/2023/01/10/genbank-sra-data-processing-webpage/
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More from our friends at #NCBI | Announcing the #GenBank and #SRA Data Processing Webpage | #OpenData #OpenScience | I like their documentation | https://ncbiinsights.ncbi.nlm.nih.gov/2023/01/10/genbank-sra-data-processing-webpage/
