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#DataStandards

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PSDI

By aligning with community standards and providing rich metadata and documentation, we can improve data longevity and reproducibility—key factors in high-impact research. Investing in open formats today means your data remains valuable for decades, supporting future scientists and AI-driven discoveries.

Let’s make data work for science, not against it. Standardize, document, and share openly to accelerate research and innovation!

#PSDI#FAIRData#OpenScience
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Gueule d'atmosphère

Real-time worldwide data sharing is a cornerstone of #meteorology. Nothing grinds to a stop (or goes into a frenzy) faster than a #weather facility gone blind and/or unable to send products. But data, instruments, requirements and the underlying tech all evolve. #DataStandards must evolve, too!

On Jan 1 the WMO declared operational a profoundly modernized data sharing infrastructure called WIS 2.0 . This all sounds unglamorous, but it's what makes everything else work.

wmo.int/media/news/wmo-informa

World Meteorological Organization · WMO Information System 2.0 will transform sharing of Earth System DataWIS 2.0 is the framework for WMO data sharing in the 21st century and makes international, regional, and national data sharing simple, effective, and inexpensive. It is based on the principle that no WMO Member should be left behind. It became operational on 1 January 2025.Real-time data sharing underpins the accuracy of weather forecasts and enhances global cooperation, but also supports vital early warning systems, aids climate research, delivers significant economic and safety benefits, and enables Earth system monitoring.  
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jonny (good kind)

literally who hurt genomics to make you all encode one specific kind of number as the ASCII characters from ! to ~ as an integer input to some logarithm function, but then others of you changed the function but kept encoding it as a single ASCII character ranging from -5 to 62 (???), and then later they decided that -5 to 62 was silly and so they changed that to 0-62 and throwing away half the original range for no reason, except actually it's 0-40 by convention.

did anyone consider "encoding it as a number"

doi.org/10.1093/nar/gkp1137

PHRED SCORES AND THE QUAL FORMAT The PHRED software reads DNA sequencing trace files, calls bases and assigns a quality value to each base called (9,10). This introduced the PHRED quality score of a base call, defined in terms of the estimated probability of error: Q_{PHRED} = -10 * log10(P_e)
ANGER FASTQ FORMAT The FASTQ format was invented at the turn of the century at the Wellcome Trust Sanger Institute by Jim Mullikin, gradually disseminated, but never formally documented (Antony V. Cox, Sanger Institute, personal communication 2009). The closest thing to an official description from Sanger can be found on the MAQ/BWA website (13,14), but even this is incomplete. Full details of the file format, describing the read title, sequence and quality scores are given later. Here, we concentrate on how the quality scores were encoded into a simple string. Early FASTQ files were used for Sanger capillary sequencing, and it was natural to use PHRED quality scores (described above). Storing PHRED scores as single characters (or bytes) gave a simple but reasonably space efficient encoding. In order that the file be human readable and easily edited, this restricted the choices to the ASCII printable characters 32–126 (decimal), and since ASCII 32 is the space character, Sanger FASTQ files use ASCII 33–126 to encode PHRED qualities from 0 to 93 (i.e. PHRED scores with an ASCII offset of 33).
An important consequence of these equations is for high values the two scores are asymptotically equal, and after rounding to the nearest integer scores of ⋛10 are interchangeable (Figure 1). However, Solexa scores go down to −5 (approximating a random read error probability of 0.75). The Sanger offset of 33 can, therefore, no longer be used. Rather, an offset of 64 was chosen, meaning ASCII 59 to 126 can be used, allowing Solexa scores from −5 to 62 inclusive.
ILLUMINA 1.3+ FASTQ FORMAT Although Illumina initially continued to use the Solexa FASTQ variant, from Genome Analyzer Pipeline version 1.3 onwards (16), PHRED quality scores rather than Solexa scores were used. However, rather than adopt the original Sanger format, Illumina introduced a third incompatible FASTQ variant designed to be interchangeable with their earlier ‘Solexa FASTQ’ files for good quality reads. The Illumina 1.3+ FASTQ variant encodes PHRED scores with an ASCII offset of 64, and so can hold PHRED scores from 0 to 62 (ASCII 64–126), although currently raw Illumina data quality scores are only expected in the range 0–40. The OBF projects refer to this variant as the Illumina 1.3+ FASTQ format, under the format name ‘fastq-illumina’ (Table 1).
#DataStandards#FileFormats#Genomics
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Miguel Afonso Caetano

#AI #GenerativeAI #Law #DataStandards: "The aim is to create the legal equivalent of an electronic healthcare patient record, that any computer system can understand and exchange. And that, argue Sali supporters, will improve lawyers’ productivity and, therefore, benefit their clients.

Established in 2017, Sali comprises legal industry professionals from large law firms, in-house corporate legal teams, legal operations, big tech companies including Microsoft, and specialist legal software providers. 

The standard is supported by industry groups such as the Corporate Legal Operations Consortium and International Legal Technology Association.

Prominent legal tech suppliers are already starting to incorporate the standard into their products, the organisation says. But it remains unclear how long this will take."

ft.com/content/9304f61a-72a2-4

Financial Times · Wanted: a data standard to underpin lawyers’ use of generative AIBy Nick Huber
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timdavies

👋 #introduction time.

I’m Tim. I spent much of last decade building, #facilitating & #maintaining #datastandards, #research projects & communities around #opendata and #opengovernment. Formerly Web Foundation, Open Data Services Co-op & Global Data Barometer.

Now at #ConnectedByData focussing on #participation, power & community voice in #DataGovernance

Freelance work w/ #LandPortal, #GlobalVoices & #opendatacoop

Also #stroud, #greenpolitics. #adoptive #parent & primary #schoolgovernor.

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Dylan Van Assche

#introduction for all the new folks here :) Welcome to the #Fediverse!

I'm Dylan Van Assche, Semantic Expert at Digitaal Vlaanderen working on #DataStandards and #KnowledgeGraphs. In my free time I'm a huge fan of #trains in various scales and a @postmarketOS Trusted Contributor working on the #mainline #Linux on #mobile and #FOSS.
Unfortunately, I still have a Twitter account for work reasons, but all my own content is posted here, on #Mastodon.

#TwitterTakeOver#Musk#Twitter
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