FSG-Treffen 19-11-20

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Flora Silvae Gabretae: FSG Technical Meeting

The meeting focussed an technical issues concerning data pipelines and web presentations of the project Flora des Böhmerwaldes – Květena Šumavy – Flora Silvae Gabretae (=FSG)

Participants

Wolfgang Diewald, Eva Holá, Petr Novotný, Martin Rohn, Marcel Ruff, Stefan Seifert, Milan Štech, Dagmar Triebel, Tanja Weibulat, Markus Weiss

Venue

SNSB IT-Zentrum
Botanische Staatssammlung München
Menzinger Str. 67
right wing of the building, groundfloor, room no. 035.
80638 München

  • Contact: Wolfgang Diewald (diewaldatsnsb.de), Tel. 089/17861253 or Dagmar Triebel (triebelatsnsb.de), Tel. 089/17861252


Getting there:

  • From Munich airport (duration about 60 min): Take S1 in the direction of 'München Hauptbahnhof'. There is a 'S-Bahn' every 20 minutes. Get off the train at the stop 'Moosach'. All stops can be found on the map 'S-Bahn, U-Bahn und Regionalzug im MVV'. At Moosach station take bus no. 51 in the direction 'Aidenbachstraße' (there is a bus every 10 minutes) and get off at 'Maria-Ward-Straße'. From here you can walk the 400 m along Menzingerstraße or otherwise take bus line 17 (direction Amalienburgstraße) and get off one stop later ('Botanischer Garten München-Nymphenburg'). Details are given under MVV Fahrplanauskunft.
  • From Munich main station (duration about 30 min): Start at 'Hauptbahnhof Süd' by taking bus 17 to 'Amalienburgstraße'. There is a bus every 10 min. Get of the bus at 'Botanischer Garten München-Nymphenburg'. Details are given under MVV Fahrplanauskunft.

WLAN: Snsb_IT_Center_4

Agenda

TOP 1 Status quo: data mobilisation (generation of new data, processing of historical data)

Czech partners, Bavarian partners


TOP 2 Status quo: occurrence data processing until data provision

(technical improvements, ABCD mapping, withhold of data not assigned to taxref-numbers)

Czech partners, Bavarian partners


TOP 3 Status quo: on management of taxonomic backbones

(challenge: names with p.p. concepts (1.400 datasets), FSG consensus backbone of taxa?

Czech partners, Bavarian partners


TOP 4 Status quo: on common web presentation of the project


TOP 5 Status quo: "in situ" floristic status categories, status values and processing

Czech partners, Bavarian partners


TOP 6 To Dos and priorities


AOB

(Internal) documentation of FSG related data pipelines and data flows?

Minutes

Responsible for minutes: Wolfgang Diewald, Marcel Ruff, with additions from all participants


TOP 1 Status quo: data mobilisation (generation of new data, processing of historical data)

  • Czech partners
    • number of records in PLADIAS: 605.000
    • number of records 2019 from Czech locations: 20.000 (will be imported in PLADIAS in spring)
    • in PLADIAS only data from Czech locations and within a 100 m range outside of the borders of Czech Republic can be managed; thus there are not very much data from Bavarian locations kept in PLADIAS and those data are under a closed license, therefore no action is necessary.
    • Further data from Bavarian locations (e. g. by M. Lepši & P. Lepši) - not kept in PLADIAS - are existing. They will be prepared and delivered to Marcel (cc: Tanja Weibulat and Wolfgang Diewald). The records will be added to BFLportal01 as far as they are from Bavarian locations. They could be provided by PLADIAS partners for DWB import in a format, as indicated under template tables.
  • Bavarian partners
    • number of records in DiversityCollection: 316.000 (< 12.000 with point coordinates)
    • number of records 2019 for the Bavarian forest region (FSG project): 7777, all with point coordinates; incl. 496 from Czech locations; Czech data will be exported and given to Milan Štech and Zdenek Kaplan, those Czech data (license CC BY) will not be imported in PLADIAS, but visualized in the common maps).
    • number of records 2019 for the Bavarian forest region (Klotz, BASG): 214, all with point coordinates
    • number of historical records to be processed in 2020 (Nationalpark Bayerischer Wald): 50.000
    • number of historical records to be quality-improved in 2020 (Florein database Diewald --> updating existing DC records): 80.000


TOP 2 Status quo: occurrence data processing until data provision

  • Czech partners
    • PLADIAS data from Czech FSG locations could be provided for GBIF as separate data publication via Diversity Workbench data pipelines. An export of PLADIAS data from Czech locations would be necessary. PLADIAS data managed in DWB for GBIF publication should met the Creative Commons CC BY 4.0 license. For data publication via GBIF, the 1/64 grid etc. data will be aggregated at GRID/Quadrant level as regularily done in the Flora of Bavaria project. Data with WGS84 coordinates will be changed to two decimals after the point (e.g. 47.574119567 to 47.57). Each data package sent to GBIF gets a DOI which can be cited.
  • Bavarian partners
    • In the near future the BioCASe guided export of BFL occurrence data (BFLportal01, BFLportal04) will be restricted on taxa which are referenced in the BFL TaxRef (Bavarian taxon reference list).
    • The ABCD mapping will be extended and the BFL TaxRef taxon-IDs will be mapped in ABCD (processed during the export session). The ABCD element "/Identification/References/Reference/" on unit level is proposed for this issue, these are the mapped ABCD Elements:
    • As far as completed, the next version of the data packages "BFLportal01" and "BFLportal04" (planned for January 2020) will include the Tax-Ref ID for each record.
      • Note 1: The suggestion to provide an export only with data converted to BFL accepted names (with their BFL TaxRef taxon-IDs) would make an additional BioCASe data pipeline for export and data provision as separate xml zip archive necessary. The Bavarian partners intend to avoid this.
      • Note 2: As a consequence the latin taxon names + TaxRef IDs in the BFLportal01, BFLportal04 data packages have to be translated to BFL accepted taxon names by the Czech partners. This has to be done by using the DTN Rest Web Service. (The BFL TaxRef list has the DP project ID: 1129).
      • Note 3: As with 2019-12-17 Stefan Seifert has extended the DTN REST Web Service (using a SQL server function) to allow for direct search for BFL TaxRef ID and get the BFL accepted taxon name, see also How to use the DWB REST Webservice for Taxon Lists.
      • Note 4: Das Auslesen der Daten für "/Identification/References/Reference/ReferenceGUID" aus dem REST Webservice erfolgt BFL spezifisch und wird in das AddOn ABCD_BayernFlora eingebaut.
    • Information on the geographic accuracy ("Unschärfe") will be exported in the future; it is planned to be shown in exact value (meters) and as text (value for quadrant). This topic is still under internal discussion.
      • For an example of “Unschärfe” (non-accuracy") concerning quadrants see Daten der Biotopkartierung
      • Accuracy of coordinates will be shown in exact value (meters)
    • It is planned to provide two new versions of the data packages "BFLportal01" and "BFLportal04" including the changes mentioned above for January.


TOP 3 Status quo: on management of taxonomic backbones

  • Czech partners
    • FSG consensus backbone of taxa for PLADIAS map presentation is hosted by Milan Štech. A current version will be - for internal use - delivered to Wolfgang Diewald. *** How many taxa? How many synonyms?***
  • Bavarian partners
    • Number of BFL taxref entities managed in DiversityTaxonNames for the Bavarian forest region (status November 2019): 1736 accepted names (1255 on species rank), ***how many synonyms?***

Further issues on BFL occurrence data pipelines with taxon names (accepted names and synonyms) managed in the BFL TaxRef list were treated under TOP 2.


TOP 4 Status quo: on common web presentation of the project

  • Requests for the modification of the web presentation can be communicated to Eva Holá (email: eva.neurazy@gmail.com).
  • Work on the FSG project website is in progress. The text will be in Czech and German, main chapters also in English. At the moment the German text ist not satisfying. The text of the main chapters should be finished and translated to German by Czech partners as soon as possible. Text blocks on the Flora von Bayern website can be used as a template. After this first level translation is done, the German language emendment, especially concerning the discipline-specific wording, will be done by Cornelia Straubinger (with assistance of Wolfgang Diewald and Dagmar Triebel).
  • Plant descriptions/characteristics will be written in Czech and then translated into German. This task has already started and is realised as free-text descriptions without fixed topic headers.
  • Alternatively, descriptions could be created in a semi-structured or structured way using management tools as DiversityDescriptions. DiversityDescriptions provides a flexible data model. Characters, character states and character groups as well as character dependencies can be defined and translations can be automatized. Examples for the use of DiversityDescriptions: Heilpflanzen-Quiz, DEEMY
  • Additional plant images taken from plants in the FSG region will be needed. Milan Štech started with imaging and collecting fotos of common plants.


TOP 5 Status quo: "in situ" floristic status categories, status values and processing

  • Czech partners
    • The floristic status will not be indicated in the maps at the FSG project website. It is being discussed whether at least a very simple status system (indigenous, not indigenous) or the concept used in PLADIAS (spontaneous, spontaneous secondary, planted, not set; see Wild et al. 2019) should be indicated in the maps. Nevertheless the floristic status (Czech concept, i.e. spontaneous, spontaneous secondary, planted, not set) will be mentioned in the plant descriptions.
  • Bavarian partners
    • A "translation" table for correct translation of status categories from DiversityCollection to PLADIAS is provided, see also Ruff et al. 2019.
    • The data package BFLportal04 has no floristic status values included.
    • The BioCASe data package BFLportal01 is providing one to several values for the floristic status of occurrence records. The first value status value is mostly assigned by the observer followed by one or several further status values as result of later status value assignments as done by scientific curatorial staff or by floristic experts. The last status value provided is the one to be used by the FSG project.
    • Note (D.T. 2019-11-29): The Bavarian partners had further internal discussions on this issue. We decided to continue to online provide all "in situ" status values. The information in the ABCD 2.06 mapping "measurement and facts" will be extended and the data have to be quality-controlled. The Analysis number field in DC will be (automatically?) filled with 1,2,3 to get the sequence information. Additional DC analysis information is mapped in ABCD, i.e., MeasurementOrFactReference mit URI, MeasuredBy, MeasurementDateTime.
    • Example (ABCD unit level, GBIF representation):
    • There was also an internal discussion how to improve the management of floristic status values in DC. In near future there will be a documentation on the management of the sequence of floristic status values for one and the same occurrence record.


TOP 6 To Dos and priorities

  • see under TOP 1-5!
  • The partners discussed the option to publish a data paper, e.g., on challenges with FSG data, with a description of the datasets and data pipelines involved and with a FSG xml-archive delivered for GFBio and GBIF added. This can easily be done in the Biodiversity Data Journal; see Biodiversity Data Journal Data Papers. It will be a technical paper which should contain aspects we discussed at this FSG meeting. The draft of this paper should be written during the second half of next year.
  • Note (D.T. 2019-12-01): One of the possible data packages to be analysed and published in this paper (FSG xml archive with ABCD structured files) should include all FSG Bohemian forest data available under CC BY license and be published in parallel via GBIF and GFBio.
  • Milan Štech will coordinate the writing of a paper in English with botanical aspects of the FSG project. This paper should be published in one of the serials of ČBS, e.g., Preslia.
  • First results of the FSG project might be presented to the Bayerische Botanische Gesellschaft in 2021.


AOB

  • The need to (internally) document the FSG-related data pipelines and data flows is emphasised.
  • The date for the submission of the first draft for the annual reports is the beginning of December. Each partner has to submit his own progress report and financial report. The progress reports should be very short. Before upload to the official project platform they should be checked by Radka Bunešová and Katka Zemanová for compliance.

Useful links

Literatur

Ruff, M., Diewald, W., Weiss, M. & Triebel, D. 2019: Floristischer Status und Florenwandel über 60 Jahre – Eine erste Analyse des Datenbestandes zum Projekt „Flora von Bayern“. In: Berichte der Bayerischen Botanischen Gesellschaft. Bd. 89, München, S. 223–244 (https:/​/​species-id.​net/​o/​media/​a/​ab/​BBBG_​89_​Floristischer_​Status_​und_​Florenwandel_​über_​60_​Jahre.​pdf).
Wild, J., Kaplan, Z., Danihelka, J., Petřík, P., Chytrý, M., Novotný, P., Rohn, M., Šulc, V., Brůna, J., Chobot, K., Ekrt, L., Holubová, D., Knollová, I., Kocián, P., Štech, M., Štěpánek, J. & Zouhar, V. 2019: Plant distribution data for the Czech Republic integrated in the Pladias database. In: Preslia. Bd. 91, S. 1–24 (electronic appendix 1+2: http://www.preslia.cz/P191WildAppendix1.pdf und http://www.preslia.cz/P191WildAppendix2.pdf – http:/​/​www.​preslia.​cz/​P191Wild.​pdf).
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