The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

ABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.info:eu-repo/semantics/publishedVersio

Workshop on Raising Data using the RDBES and TAF (WKRDBESRaiseTAF; outputs from 2022 meeting)

41 páginasThe Workshop on Raising Data using the RDBES and TAF (WKRDBES-Raise&TAF) met online (26–30 of September 2022) to evaluate the use of the Regional Database and Estimation System (RDBES) format to reproduce the 2022 InterCatch input and output, identifying a Transparent Assessment Framework (TAF) structure to organize the intermediate steps and to propose standardized output formats. The main outcomes of WKRDBES-Raise&TAF were: · RDBES provides sufficient support for current national estimation protocols. However, some minor issues were reported that hampered an exact reproduction of the estimates. Therefore, adaptations of the data model should not be excluded completely. · All the input to stock assessment that InterCatch currently provides, could be reproduced. The participants started from the current stock extracts that can be downloaded from InterCatch. · A workflow was proposed with a national TAF repository for each country, a stock estimation repository and a stock assessment repository. The intermediate output of those repositories will be stored in an ‘intermediate output database’ and depending on the user role, you will get access to the relevant stages in this workflow. · The following requirements for the standard output formats were defined: they cannot be more restrictive than the InterCatch input and output format; they should present measures of uncertainty and sample sizes (for national estimates) and should have a configurable domain definition (for national estimates). Despite those successful outcomes, the current plan for transition to an operational system was concluded to be too optimistic. WKRDBES-Raise&TAF therefore recommends to the Working Group on Governance of the Regional Database and Estimation System (WGRDBESGOV) to revise the roadmap and allow RDBES to be in a test phase also for 2023. WKRDBES-Raise&TAF felt the need to test the proposed workflow on a small scale and therefore recommends to the WGRDBESGOV to arrange a workshop where two stocks (pok.27.3a46 (Saithe (Pollachius virens) in Subareas 4, 6 and Division 3.a (North Sea, Rockall and West of Scotland, Skagerrak and Kattegat) and wit.27.3a47d (Witch (Glyptocephalus cynoglossus) in Subarea 4 and Divisions 3.a and 7.d (North Sea, Skagerrak and Kattegat, eastern English Channel)) will be set up to go through the whole flow.Peer reviewe

Design of an online health-promoting community : negotiating user community needs with public health goals and service capabilities

Background An online health-promoting community (OHPC) has the potential to promote health and advance new means of dialogue between public health representatives and the general public. The aim of this study was to examine what aspects of an OHPC that are critical for satisfying the needs of the user community and public health goals and service capabilities. Methods Community-based participatory research methods were used for data collection and analysis, and participatory design principles to develop a case study OHPC for adolescents. Qualitative data from adolescents on health appraisals and perspectives on health information were collected in a Swedish health service region and classified into categories of user health information exchange needs. A composite design rationale for the OHPC was completed by linking the identified user needs, user-derived requirements, and technical and organizational systems solutions. Conflicts between end-user requirements and organizational goals and resources were identified. Results The most prominent health information needs were associated to food, exercise, and well-being. The assessment of the design rationale document and prototype in light of the regional public health goals and service capabilities showed that compromises were needed to resolve conflicts involving the management of organizational resources and responsibilities. The users wanted to discuss health issues with health experts having little time to set aside to the OHPC and it was unclear who should set the norms for the online discussions. Conclusions OHPCs can be designed to satisfy both the needs of user communities and public health goals and service capabilities. Compromises are needed to resolve conflicts between users’ needs to discuss health issues with domain experts and the management of resources and responsibilities in public health organizations

Design of an online health-promoting community : negotiating user community needs with public health goals and service capabilities

Background An online health-promoting community (OHPC) has the potential to promote health and advance new means of dialogue between public health representatives and the general public. The aim of this study was to examine what aspects of an OHPC that are critical for satisfying the needs of the user community and public health goals and service capabilities. Methods Community-based participatory research methods were used for data collection and analysis, and participatory design principles to develop a case study OHPC for adolescents. Qualitative data from adolescents on health appraisals and perspectives on health information were collected in a Swedish health service region and classified into categories of user health information exchange needs. A composite design rationale for the OHPC was completed by linking the identified user needs, user-derived requirements, and technical and organizational systems solutions. Conflicts between end-user requirements and organizational goals and resources were identified. Results The most prominent health information needs were associated to food, exercise, and well-being. The assessment of the design rationale document and prototype in light of the regional public health goals and service capabilities showed that compromises were needed to resolve conflicts involving the management of organizational resources and responsibilities. The users wanted to discuss health issues with health experts having little time to set aside to the OHPC and it was unclear who should set the norms for the online discussions. Conclusions OHPCs can be designed to satisfy both the needs of user communities and public health goals and service capabilities. Compromises are needed to resolve conflicts between users’ needs to discuss health issues with domain experts and the management of resources and responsibilities in public health organizations

Multilingual comparable corpora of parliamentary debates ParlaMint 4.0

ParlaMint 4.0 is a set of comparable corpora containing transcriptions of parliamentary debates of 29 European countries and autonomous regions, mostly starting in 2015 and extending to mid-2022. The individual corpora comprise between 9 and 126 million words and the complete set contains over 1.1 billion words. The transcriptions are divided by days with information on the term, session and meeting, and contain speeches marked by the speaker and their role (e.g. chair, regular speaker). The speeches also contain marked-up transcriber comments, such as gaps in the transcription, interruptions, applause, etc. The corpora have extensive metadata, most importantly on speakers (name, gender, MP and minister status, party affiliation), the political parties and parliamentary groups (name, coalition/opposition status, Wikipedia-sourced left-to-right political orientation, and CHES variables, https://www.chesdata.eu/). Note that some corpora have further metadata, e.g. the year of birth of the speakers, links to their Wikipedia articles, their membership in various committees, etc. The transcriptions are also marked with the subcorpus they belong to ("reference", until 2020-01-30, "covid", from 2020-01-31, and "war", from 2022-02-24). The corpora are encoded according to the Parla-CLARIN TEI recommendation (https://clarin-eric.github.io/parla-clarin/), but have been encoded against the compatible, but much stricter ParlaMint encoding guidelines (https://clarin-eric.github.io/ParlaMint/) and schemas (included in the distribution). This entry contains the ParlaMint TEI-encoded corpora and their derived plain text versions along with TSV metadata of the speeches. Also included is the 4.0 release of the sample data and scripts available at the GitHub repository of the ParlaMint project at https://github.com/clarin-eric/ParlaMint. Note that there also exists the linguistically marked-up version of the 4.0 ParlaMint corpus, also linked with concordancers, which is available at http://hdl.handle.net/11356/1860. As opposed to the previous version 3.0, this version adds corpora for Spain (ES), Finland (FI) and the Basque Country (ES-PV); extends the corpora for Austria (AT), Czechia (CZ), Hungary (HU), and Ukraine (UA) with more recent data; adds metadata to political parties and parliamentary groups on left-to-right political orientation from Wikipedia as well as CHES variables; and adds the information on whether a speaker was a minister and when for the corpora that previously lacked this information. The TEI encoding of some details has also changed, and many errors found in 3.0 corpora have been corrected

Linguistically annotated multilingual comparable corpora of parliamentary debates ParlaMint.ana 4.0

ParlaMint 4.0 is a set of comparable corpora containing transcriptions of parliamentary debates of 29 European countries and autonomous regions, mostly starting in 2015 and extending to mid-2022. The individual corpora comprise between 9 and 126 million words and the complete set contains over 1.1 billion words. The transcriptions are divided by days with information on the term, session and meeting, and contain speeches marked by the speaker and their role (e.g. chair, regular speaker). The speeches also contain marked-up transcriber comments, such as gaps in the transcription, interruptions, applause, etc. The corpora have extensive metadata, most importantly on speakers (name, gender, MP and minister status, party affiliation), the political parties and parliamentary groups (name, coalition/opposition status, Wikipedia-sourced left-to-right political orientation, and CHES variables, https://www.chesdata.eu/). Note that some corpora have further metadata, e.g. the year of birth of the speakers, links to their Wikipedia articles, their membership in various committees, etc. The transcriptions are also marked with the subcorpus they belong to ("reference", until 2020-01-30, "covid", from 2020-01-31, and "war", from 2022-02-24). The corpora are encoded according to the Parla-CLARIN TEI recommendation (https://clarin-eric.github.io/parla-clarin/), but have been encoded against the compatible, but much stricter ParlaMint encoding guidelines (https://clarin-eric.github.io/ParlaMint/) and schemas (included in the distribution). The ParlaMint.ana linguistic annotation includes tokenization; sentence segmentation; lemmatisation; Universal Dependencies part-of-speech, morphological features, and syntactic dependencies; and the 4-class CoNLL-2003 named entities. Some corpora also have further linguistic annotations, in particular PoS tagging according a language-specific scheme, with their corpus TEI headers giving further details on the annotation vocabularies and tools used. This entry contains the ParlaMint.ana TEI-encoded linguistically annotated corpora; the derived CoNLL-U files along with TSV metadata of the speeches; and the derived vertical files (with their registry file), suitable for use with CQP-based concordancers, such as CWB, noSketch Engine or KonText. Also included is the 4.0 release of the sample data and scripts available at the GitHub repository of the ParlaMint project at https://github.com/clarin-eric/ParlaMint and the log files produced in the process of building the corpora for this release. The log files show e.g. known errors in the corpora, while more information about known problems is available in the (open) issues at the GitHub repository of the project. This entry contains the linguistically marked-up version of the corpus, while the text version, i.e. without the linguistic annotation is available at http://hdl.handle.net/11356/1859. As opposed to the previous version 3.0, this version adds corpora for Spain (ES), Finland (FI) and the Basque Country (ES-PV); extends the corpora for Austria (AT), Czechia (CZ), Hungary (HU), and Ukraine (UA) with more recent data; adds metadata to political parties and parliamentary groups on left-to-right political orientation from Wikipedia, as well as CHES variables; adds the information on whether a speaker was a minister and when for the corpora that previously lacked this information. The TEI encoding of some details has also changed, and many errors found in 3.0 corpora have been corrected. Furthermore, the vertical files (and hence the individual corpora available on the concordancers) have their meta-data in the local language of the corpus, and not English