NFDI4BioDiversity

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Dokumente wg. Begutachtung: https://drive.google.com/drive/folders/1CtWJyiCrhvLFXtvseGns-gBokaNu5IQp?usp=sharing


There is an increasing demand of funders, publishers and research organisations to evaluate data as FAIR and services as trusted and certificated. This forces data centers, data archives and data repositories of all kind (domain or subject-based, institutional, national, research-project-based etc.) to be formally accredited to offer high-quality data and certificated services. Certifications by organisations like the ICSU-WDS, DINI e.V., nestor, or CoreTrustSeal have become widespread means. Based on our long-term experiences with the certification of the PANGAEA information system, our essential role in the development of the CoreTrustSeal, our involvement in the H2020 FAIRsFAIR project, and on-going efforts on CoreTrustSeal certification of the GFBio data centers, NFDI4BioDiversity is in a prime position to share this knowledge, develop strategies for certification and guide the certification process in upcoming data repositories and other NFDI consortia as well. Certification will address authenticity, integrity, confidentiality, and availability of data and services as well as the assessment of the FAIRness of data centers and their holdings. This cross-cutting topic also include certification strategies for software pieces and will be addressed in TA 3.


Telco NFDI4BioDiversity Coordination 15.8.2019

Thema Arbeitsprogramm: Template f. Measures (Vorschlag v. Birgit: https://docs.google.com/document/d/1bobeOW_S9Nd6AbDIz7q56ntQQpOAO-Hw1Lonz7WSPd0/edit?usp=sharing Struktur Umfang - Seitenanzahl Fussnoten Verzahnte Measures - Referenzierungen Cross NFDI measures Liste der Measures b. denen BioDiversity im Lead ist: https://docs.google.com/document/d/1NWxfcXlH7r7b7C25pULD5w10uxsqMjy7O-9O4N2V8tg/edit?usp=sharing Weiteres Vorgehen timeline Finanzen - co-applicants, participants


Support letters table: https://docs.google.com/spreadsheets/d/1NFJef9MwsVQGjGRmbedXKcAH1Et6C6-lgC9_OPq4YuI/edit#gid=0


email 29.8.19: hier nochmals zum Selbststudium die heute gezeigte Tabelle zu Finanzen in Google. https://docs.google.com/spreadsheets/d/1VtspzI_aRl9qvZsWMSLruCTx6_DvHlYnS3AoRSIItII/edit?usp=sharing

CVs und LoC Template: https://drive.google.com/drive/folders/1z9_B8MVH4WcaWedXS8e_89sudJXmCO48?usp=sharing


email 22.8.19: Template für die LoS: https://docs.google.com/document/d/1t_Bqp5D2ioeNSY8-AwuOPrv5ExD_i8JLu9YYfxzaEcg/edit


Berlin Treffen 15.8.19 von 11 NFDI Konsortien, "Nachlese" 21.8.19: https://docs.google.com/document/d/130H37RGkVLtb9_57z-zwlT5UrBETYLdDS8zbU0a9B2I/edit?usp=sharing


NFDI4BioDiversity Coordination Team Telcos: Browser: https://conf.dfn.de/webapp/conference/97959265 Telephone: Call: 0049 30 200 97959265 Professional Videoconference System (H.323): Call: 004910097959265

I recommend installing the Infinity connect client see https://support.pexip.com/hc/en-us/articles/360015877891-Infinity-Connect-Client-Download


5.8.19: Shared folder https://drive.google.com/drive/folders/1lZyd_zSjPgEAsh7kfFv5Yudc3xflKcDl


1.8.19: https://docs.google.com/document/d/1qhXfat4r0ccOkg0ZMXfdUYO8Nogm4xioppRYkybJd5M/edit?usp=sharing

Doc, gesandt von Frank Oliver, 31.7.19, veraltet: https://docs.google.com/document/d/1MVKPj29l9oAgDU9HUNbbBKjNV_E2fE5MMyhuLN11J8k/edit?usp=sharing


DFG LoI: https://docs.google.com/document/d/12ulNwVQ3G-UMeYR7DKYAN5iqEbAklJsHQ4Seuh77N88/edit?usp=sharing


Google Doc "NFDI4BioDiversity Community Workshop": https://docs.google.com/document/d/1Zescgas0jILOYiz0fYV6FlsgVKeM688ugzxYCnQKWLI/edit?usp=sharing


Hallo Mitstreiter, zunächst vielen Dank für die tolle Zuarbeit zum 6-Seiter für die DFG NFDI Konferenz im Mai.

Die aktuelle - gekürzte - praktisch finale Version ist jetzt hier zu finden: https://docs.google.com/document/d/1BMUmNVFFhwWhN3tWup_g28fJN0t5zNCGq60kG8HxmRM/edit?usp=sharing

Folgende Anmerkungen bitte ich zu beachten:

1. Wir mussten einiges kürzen um die Vorgabe der DFG einzuhalten.

2. Das ist nicht der Antrag, das ist nur eine unverbindlichen Absichtserklärung - d.h. wenn jemand sich nicht perfekt repräsentiert fühlt - im Antrag ist dann mehr Platz dafür.

3. Im GDoc ist auf Seite 4 der Link zum formatierten PDF - d.h. bitte im GDoc nicht auf Formatierung achten, das mache ich alles im Wordfile - die Anzahl der Seiten im GDoc stimmt deshalb auch nicht.

4. Die Graphik wird sich vermutlich in den nächsten Tagen noch ändern - sobald wir mit der Uni-Bremen gesprochen haben

5. Ganz wichtig: Bitte, nur noch echte Fehler korrigieren - wie Ihr im PDF seht ist der Text genau auf die 6 Seiten hingetrimmt - da hat an sich kein zusätzliches Wort mehr Platz - es gilt Punkt 2!

6. Noch wichtiger: Bitte überprüft Eure Zugehörigkeiten auf den Seiten 1 und 2.

Noch eine Bemerkung zu Punkt 6, damit sich keiner wundert.

Ich habe mir erlaubt unter Participating research insitutions auch die Universitäten zu nennen bei denen die Professuren der Leiter der Infrastrukturen (wie GWDG, DSMZ etc.) angesiedelt sind, da ich davon ausgehen, dass die entsprechenden Leiter auch an den jeweiligen Universitäten aktiv das Thema Forschungsdatenmanagement mitgestalten. Wenn jemand das nicht möchte, bitte melden.

Deadline für Rückmeldungen ist Mittwoch der 27.03, 16:00 - strikt, damit ich Zeit habe die finale Version zu erstellen mit dem Ziel sie spätestens am 29.03 einzureichen.

Eine erfolgreiche Woche wünsche ich.

Frank Oliver





1. Outline 6-Seiter https://docs.google.com/document/d/15-EihUZ3uxksjeGwqaMVZcuGoJfzn5NYRIvV3Y9SiRE/edit?usp=sharing

2. Partnerliste: https://docs.google.com/document/d/1M39jtukgA9qiY1rVGY0V6dcX18mEV5CBeMxLaDePUoM/edit?usp=sharing


ToDos:

1. Im 6-Seiter haben wir bestimmte Abschnitte bestimmten Personen zugeordnet. D.h. jetzt nicht, das nur die arbeiten müssen. Das ist so gedacht, dass diese Personen die Kommentare einsammeln und den Ihnen zugeordneten Abschnitt konsolidieren. In Anbetracht der Kürze des Dokumentes ist folgendes zu beachten:

Prägnanz vor Vollständigkeit Kürzen vor erweitern Listings in Text überführen (wo sinnvoll) Lead soll konsolidieren und harmonisieren - alle anderen sind aufgefordert ihre Expertise einzubringen Deadline Mittwoch, 13.03.2019

2. Wir haben bereits mehrere Anfragen von möglichen weiteren Partnern/Beteiligten bekommen. Diese sind im Partner Dokument gekennzeichnet und (bis aufs ZMT, das kam erst heute) gibt es auch kurze Einseiter die wir abgefragt haben um ihre Expertise und Wünsche zu formulieren. Über eine Aufnahme in NFDI4Biodiveristy müssen wir uns zeitnah abstimmen. Bitte kommentiert im Partnerdokument, ob ihr dafür oder dagegen seid. Deadline Mittwoch, 13.03.2019


Textbausteine für LoI

Among the data management services implemented as part of GFBio are software and services for the management of regionalised or subdomain-specific taxonomic backbones and tools for the management of generic and specific data exchange schemes and their mapping and conversion with evolving comprehensive (meta-)data standards. These tools are essential in order to fulfil dynamic demands of subdisciplinary compatibility within the biodiversity research domain and across. NFDI4BioDiversity will address further software development together with the management of evolving discipline-specific standards for data exchange in biodiversity informatics, geo informatics and laboratory informatics. The efforts will include partners involved in disciplien-specific nomenclatural and standardisation committees and partners involved in cross-discipline working groups of international standards organisations and national standards bodies.


Among the data management services implemented as part of GFBio are software and services for the management of regionalised or subdomain-specific taxonomic backbones and tools for the management of generic and specific data exchange schemes and their mapping and conversion with evolving comprehensive (meta-)data standards. These tools are essential in order to fulfil dynamic demands of subdisciplinary compatibility within the biodiversity research domain and across. NFDI4BioDiversity will address further software development together with the management of evolving discipline-specific standards for data exchange in biodiversity informatics, geo informatics and laboratory informatics. The efforts will include partners involved in disciplien-specific nomenclatural and standardisation committees and partners involved in cross-discipline working groups of international standards organisations and national standards bodies.


Standardization (cooperation with standards bodies for technical standards and norms)

Together with NFDI4Life NFDI4BioDiversity is planning to cooperate with national and international standardisation organisations in the field of developping technical formats and norms regarding data exchange in areas of geoinformatics, laboratory informatics and biodiversity informatics. Standardisation organisations include World Standards Cooperation (WSC), World Wide Web Consortium (W3C), ASTM International and DIN e.V.



Anm-. Diepenbroek

"DWB tools for data mobilisation (e.g. experimental studies, monitoring projects) DWB data brokerage …"


Hallo Dagmar - damit habe ich ein Problem. Das sind eher Mittel, die wir einsetzen, um Daten zu mobilisieren oder public zu machen



DWB software installations are used for major citizen science projects, e.g. Flora of Bavaria. DWB might build services for data exchange and taxonomic backbone access together with an upcoming Living Atlas project. DWB software installations are used by 3 GBIF nodes and 3 GFBio collection data centers, i.e. SNSB, SMNS, ZFMK and the GBOL data network.(e.g., with data exchange interface for ABCD standard) DWB software installations are used by the freely available DWB REST Webservice for Taxon Lists (infos about the content under http://www.diversitymobile.net/wiki/DTN_Taxon_Lists_Services) (e.g., with data exchange interface for DwC standard) DWB software installations are used to manage community standard schema and data model development, e.g. MOD-CO schema, see publication (doi.org/10.1093/database/baz002) DWB software installations are used as database backbone for descriptive data as of LIAS and DEEMY data repositories, www.lias.net and www.deemy.de (e.g., with data exchange interface for SDD standard).







NFDI4Life

https://docs.google.com/document/d/1G9dbNMc4cRnaPT-M7_ZWctY4Y5sGNu__DCCmBeasO9A/edit?usp=sharing



Text 29.8.19 aus https://docs.google.com/document/d/1qhXfat4r0ccOkg0ZMXfdUYO8Nogm4xioppRYkybJd5M/edit?ts=5d5f81c3# p. 61 bis 63


TA1 M2: Back office support with tools/platforms for gathering, structuring and (early) mobilization of data, tools for project data management, analyses, modeling, sharing, networking, education – curricula

(GFBio e.V. and …. and … and ... Jena?, SNSB?)

Lead: ???

Description: The Biodiversity communities are diverse in their research approaches. Some working groups are small (a prof with 1-3 universitary researchers) otheres arel large groups of academic and/ or volunteer experts which collaborate in research and citizen science networks of hundreds of persons. With this as background NFDI4BioDiversity has to address a wide array of tools for (a) gathering, structuring and managing raw data, (b) tools for realising scientific workflows in the field and lab (c) analysing and modelling biodiversity data (d) creating joint virtual research environments for networking and sharing project data (d) publishing data and (e) archiving biodiversity data objects. Some communities are used to rely on spreadsheets tools, like MS Excel for diverse workflow steps in the field and lab, others use one of the more than 200 commercial LIMS and ELNs in their molecular labs or use a combination of several tools. Most groups are not focussed on the long-term management of their data but on the ad hoc analysis of own and foreign data. Thus, we have a wide spectrum of thousands of analysis tools (see e.g. under bio.tools) and only a minor number of scientific workflow management tools. Collaborative work is hitherto either restricted to a late time of the research process (data life cycle) with a paper in mind (e.g. using Pensoft Arpha tool, Citavi and publishers services) or might be forced by the use of common digital or non-digital resources as in an education, training, outreach, monitoring or virtual collection project. The latter projects often have a domain-specific data portal, guided data entry and data access regarded as cooperative work. More generic are those based on the Living Atlasses platform, https://living-atlases.gbif.org/ , LTER-D platform, Jupyter Lab for Jupyter Notebooks or OSF platform. Tools which are proved to be appropriate for long-term data management and archiving purposes and are in use by German biodiversity data centers are documented by GFBio, see https://gfbio.biowikifarm.net/wiki/Technical_Documentations and part of TA3. As part of the biodiversity research communities we have two software engineering groups in Germany which are developing appropriate management software for years. They offer widely used software suites for early data mobilisation and managing primary research data. Diversity Workbench (DWB) is a suite of relational SQL databases and tools for single researchers as well as for institutional data repositories to process bio- and geodiversity data (see DWB in bio.tools under https://bio.tools/t?page=1&q=DWB&sort=score). DWB tools address data generation, data management, quality assurance and basic data analysis issues in the following scientific domains: molecular and evolutionary biology, systematics, biogeography, ecological and environmental sciences, geosciences. The desktop tools (client-server database applications, data processing and GIS tools) and the mobile app are independent of each other, but might be joint to build a linked data network. DWB offers central cloud services with terminologies, taxonomies, regional taxon checklists, gazetteers and GIS information. The software has been user-tested for more than 20 years, see regular DWB workshops. DWB use is free and without costs. The software is open source apart from the underlying MS operating system and MS SQL Server. BEXIS 2 is a data management software supporting researchers in documenting, finding, sharing, and publishing data during the active phase of a research project. BEXIS 2 is a modular, scalable, interoperable, free and open source system supporting large research consortia on all aspects of data life cycle management. The software is being developed based on requirements of the biodiversity and ecology domain that mostly deal with tabular data, but is generic enough to serve other domains and data types as well. BEXIS 2 and DWB are described under https://www.gfbio.org/tools. DWB database suite has more than 200 users with accounts at the SNSB IT Center and a high number of unknown users with local installations. It is used by more than 30 organisations and large projects, see http://www.snsb.info/PartnerOrganisations.html . DWB software installations are used for major citizen science projects, e.g. Flora of Bavaria and Spiders of Germany. DWB might build services for data exchange and taxonomic backbone access together with an upcoming Living Atlas project. DWB software installations are used by 3 GBIF nodes and 3 GFBio collection data centers, i.e. SNSB, SMNS, ZFMK and the GBOL data network.(e.g., with data exchange interface for ABCD standard) DWB software installations are used by the freely available DWB REST Webservice for Taxon Lists (infos about the content under http://www.diversitymobile.net/wiki/DTN_Taxon_Lists_Services) (e.g., with data exchange interface for DwC standard) DWB software installations are used to manage community standard schema and data model development, e.g. MOD-CO schema, see publication (doi.org/10.1093/database/baz002) DWB software installations are used as database backbone for descriptive data as of LIAS and DEEMY data repositories, www.lias.net and www.deemy.de (e.g., with data exchange interface for SDD standard). With the great technical diversity of the software ecosystem in mind, NFDI4Biodiversity will build a network of expertise with bioinformatics, ecoinformatics and biodiversity informatics persons who have a broad background in relevant tools for data analysis in biodiversity research and biology. Some members of this team should be employed on a permanent position and work together with external experts from software engineering groups (see above) and existing major data initiatives and evolving NFDI4BioDiversity use cases as described under TA1. The team members of measure M2 will give technical advice to TA1 M1 research groups and citizen science monitoring projects optimally already during the process of designing a research project and writing a DFG proposal. In addition, they will give IT support to single researchers as well as to existing large projects which want to migrate from obsolete infrastructures to new technical solutions (without loss of data!). They will help with software installations and the use of NFDI4BioDiversity cloud services and will build the technical help desk for supported use cases.

Prerequirements:

experience from two software engineering groups and GFBio project

Specific goals and targets:

technical support for large projects of TA1 use cases, single researchers and research groups

Methods used:

installations of DWB and BEXIS 2, biowikifarm, JIRA For internal documentation, cooperation and communication the team will rely on the experience in GFBio and use a combination of the ticket system JIRA, two Wikis set up in the biowikifarm and a GITHub. M2 will be involved in the exchange of technical standards/ code exchange with other NFDIs.


TA1 M3: Front office/ Back office data science support by scientific data managers

Lead: ???

(GFBio e.V. and …. and … and ... Jena?, SNSB?)

Description: The data management strategy of NFDI4BioDiversity strongly relies on a close cooperation between the consortium and the providers as well as the consumers of data. This includes all stages of the data life cycle and all stages of the research process with assigned data pipelines. With the experience from GFBio and GFBio e.V. we realise that there are a number of general scientific data management issues which have to be addressed and communicated with providers and consumers of data or data managers in large DFG-funded SFBs. It has to be done individually by user help desk persons. It concerns guidelines and legal regulations for environmental and biology data and material (context CBD, ABS, nature conservation regulations etc.), IPR and licences as well as the world of evolving community-agreed content schemas and standards for mobilising, exchanging and archiving biodiversity data and metadata. This also concerns the structuring of data, data quality and enrichment, e.g. by using standard vocabularies and ontologies and the correct use of NFDI4BioDiversity submission templates. Thus, the direct contact with the user is essential and requires a NFDI4BioDiversity user help desk run by experts for manual curation of scientific data, validation of data and transforming of data. Those experts have to be from various domains within the wide field of taxonomic research, ecology, environmental science and (molecular) biodiversity research.

Prerequirements:

experience from GFBio e.V. and GFBio project with scientific curators

Specific goals and targets:

domain-specific support for scientific data curation for single researchers and small research groups

Methods used:

installations of biowikifarm, JIRA, GFBio submission tool, connected to data centers, using established GFBio infrastructure, e.g. TerminologyService, installations of DWB and BEXIS 2 at data centers For internal documentation, cooperation and communication the team will rely on the experience in GFBio and use a combination of the ticket system JIRA, two Wikis set up in the biowikifarm and a GITHub. M3 will be involved in the exchange of content standards/ and vocabularies/ ontologies with other NFDIs.



DWB software installations are used for major citizen science projects, e.g. Flora of Bavaria and Spiders of Germany. DWB might build services for data exchange and taxonomic backbone access together with an upcoming Living Atlas project. DWB software installations are used by 3 GBIF nodes and 3 GFBio collection data centers, i.e. SNSB, SMNS, ZFMK and the GBOL data network.(e.g., with data exchange interface for ABCD standard) DWB software installations are used by the freely available DWB REST Webservice for Taxon Lists (infos about the content under http://www.diversitymobile.net/wiki/DTN_Taxon_Lists_Services) (e.g., with data exchange interface for DwC standard) DWB software installations are used to manage community standard schema and data model development, e.g. MOD-CO schema, see publication (doi.org/10.1093/database/baz002) DWB software installations are used as database backbone for descriptive data as of LIAS and DEEMY data repositories, www.lias.net and www.deemy.de (e.g., with data exchange interface for SDD standard).



In parallel TA4 M1 will cooperate with TA 3 M3 to consolidate and extend the existing GFBio technical network of data providers and services. The productive services for biodiversity (occurrence) data at the GFBio data centers will be extended by NFDI4BioDiversity community-standard-compliant REST APIs with RDF framework installed at the single data providers´ webservers and corresponding services in the RDC environment with dynamic database indices and caching set up in TA4 M3. In this context TA3 M2, TA3 M3, TA4 M1, TA4 M2 and TA4 M3 will closely work together to develop a guideline on “How to implement and how to consume REST APIs for NFDI4BioDiversity RDC”.



NFDI4BioDiversity Kurzantrag: https://docs.google.com/document/d/1PYXB8Au0lCd9Uljc2qfoGClkjvSHlhMPXJR9r5F1pPw/edit?usp=sharing