#MyBibliography #NCBI
Are any other NIH funded scientists out there having trouble with their NIH NCBI My Bibliography? Mine went crazy this past week, generating dozens of duplicates over and over again, forgetting about Public Access Compliance status, not retaining changes, etc.
(I might not have otherwise noticed it, except that NSF recently required biosketches only be submitted using NCBI SciENcv, which gets publications from NCBI My Bibliography, so it’s a bit of a nightmare.)

Idea: make a script to search papers for accessions/links to #NCBI, and check if the data is actually public. #OpenData

Super excited to see that serratus.io has consumed the #SRA, part of project STRIDES to put all #ncbi data on AWS and GCP

"A comparison between Greengenes, SILVA, RDP, and NCBI reference databases in four published microbiota datasets"

https://www.biorxiv.org/content/10.1101/2023.04.12.535864v1

#16S #metabarcoding #MarkerGeneSequencing #SequenceDatabase #db #Greengenes #SILVA #RDP #NCBI #microbiome

A few days ago I discovered that the My Bibliography section of My #NCBI had suddenly duplicated almost all of my publications. Because the system is so poorly designed and buggy, it took me a few hours to delete the duplicates.

Today I discovered that all (?) of the duplicates have returned. Given that #NIH wants us to be using it to do things like declare access compliance, they need to get the system working properly.

Anyone have a clue what's going on here?

A bit more detailed on how to navigate genome alignments on CGV (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) :) #comparativegenomics #NCBI
https://youtu.be/_TA86Tu1N0c

is there a way to suggest a new link dbsnp ↔️ pubmed to the #ncbi ?

#variant #pubmed #ncbi

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

I need to download genome sequences occasionally (often enough to be annoying, not often enough to be "good" at it) and it used be a real hassle. The fine folks at #NCBI did a nice job at creating a new datasets portal (https://www.ncbi.nlm.nih.gov/datasets/) enabling commands like this to get whole genome datasets:

`datasets download genome accession GCF_000146045.2 --include genome --filename GCF_000146045.2.zip`

commands that they also helpfully provide on each page.

Does anyone know if there is a up-to-date count of (human) RNAseq and / or microarray samples in #GEO / #SRA #NCBI?

My best estimate comes from #recount3 which processed 750,000 but I wonder if there is more to process, or if that number is the most up-to.date.
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02533-6

Alternatively, is there a way to query this?

cc' @benlangmead

RT @laing_simon@twitter.com

First-Attempt Intubation Success Among Emergency Medicine Trainees by Laryngoscopic Device and Training Year: A National Emergency Airway Registry Study - PubMed #ncbi https://pubmed.ncbi.nlm.nih.gov/36669924/

🐦🔗: https://twitter.com/laing_simon/status/1617138848420581381

PubMed keeps throwing 500 errors this morning.

#science #biology #NCBI #PubMed

@florian_krammer GISIAD is not a public repository. It requires individuals to agree to restrictive conditions to access data that limit use and prevent access by anyone who disagrees with their conditions. It is not open science. #NCBI has none of those conditions for accessing sequence data. If someone wants to submit sequence data to GISAID, fine (we do). But please also submit your data to NCBI to ensure true open access by all.

I saw #NCBI 's post about the #BLAST scaling problem. What if we replaced the #LMDB backend with an in memory database like #Redis? This could reduce latency by avoiding Disk I/O and improve scalability through sharding/threading. Not sure how big the current dataset is/will be but #aws offers EC2 instances with up to 24 TiB of RAM engineered specifically for low latency.

Is LMDB the bottleneck, or is the corpus of nt's just too large to search quickly? Would love to hear thoughts on this

"#PubMed Update: Proximity Search Now Available in PubMed" https://www.nlm.nih.gov/pubs/techbull/nd22/nd22_pubmed_proximity_search_available.html

To create a proximity search in PubMed, enter terms using the following format:

"search terms"[field:~N]

Search terms = Two or more words enclosed in double quotes.
Field = The search field tag for the [Title] or [Title/Abstract] fields.
N = The maximum number of words that may appear between your search terms.

#ncbi #eutils

🧵Combining & aligning the only available #Mubende 2022 #Ebola #UVRI shared sequence with all #SUDV sequences from #NCBI I've #computed this #phylogenetic_tree that indicates #intriguing #similarity with the #still_perplexing #2011 #Nakisamata (#Luwero) "outbreak". Some thoughts:

🧵Combining & aligning the only available #Mubende 2022 #Ebola #UVRI shared sequence with all #SUDV sequences from #NCBI I've #computed this #phylogenetic_tree that indicates #intriguing #similarity with the #still_perplexing #2011 #Nakisamata (#Luwero) "outbreak". Some thoughts:

🧵Combining & aligning the only available #Mubende 2022 #Ebola #UVRI shared sequence with all #SUDV sequences from #NCBI I've #computed this #phylogenetic_tree that indicates #intriguing #similarity with the #still_perplexing #2011 #Nakisamata (#Luwero) "outbreak". Some thoughts:

Does anybody know of any well characterized serine or threonine phosphomimetic (change to Asp or Glu) missense variants in #ClinVar ? I took a first pass to match against known phosphosites in humans but didn't come up with much.

#genetics #NCBI #signaling

Interesting, due to #BigData scaling problems #NCBI are considering splitting up the massive #BLAST NT nucleotide database into chunks like Eukaryotic, Prokaryotic, Virus, and synthetic/other https://ncbiinsights.ncbi.nlm.nih.gov/2022/11/17/re-evaluating-blast-nucleotide-nt/ - they invite feedback