Implementation of the information system BExIS 2 at the UFZ: Quality control, retrieval and sharing of [biodiversity] data

Transcription

1 Implementatin f the infrmatin system BExIS 2 at the UFZ: Quality cntrl, retrieval and sharing f [bidiversity] data Dr. Mark Frenzel Helmhltz Centre fr Envirnmental Research - UFZ

2 Best practice elements and gals in data management AIM: Reuse f data! Matter f attitude f peple Recgnitin f imprtance f data management Tp dwn and Bttm up! Availability and Open access t data Defined wrkflws (acquisitin-quality cntrl-strage-publicatin) Dcumentatin and selectin f relevant data sets Meta data standard fr data descriptin IT issues Thesauri (cntrlled vcabulary) Persistent strage / hardware Magic tls: sftware slutins

3 Best practice elements and gals in data management Final step: DOI Data publicatin f relevant data sets Linking data t publicatins and peple Feed back n willingness f data prviders Smiling data creatrs Smiling users

4 The issue f bidiversity data Mstly persn-generated data! Hetergeneity f data Lgic f eclgists related t data (different frm IT peple) Eclgy: data based n spreadsheets Data base?! Quality cntrl Plausibility tests Expert knwledge Sftware (e.g. ccurrence f species A at lcatin B plausible?) Technical cnsistency Crrect data types Crrect cell entries

5 BExIS - a generic data management tl fr bidiversity data Bidiversity Explratries Infrmatin System BExIS 1: Develpment started with DFG prject Bidiversity Explratries (2006) infrmatin management system, prject data base Instances: DFG Bidiversity Explratries, DFG Jena Experiment, DFG Research Grup: Kilimanjar, DFG Cllabrative Research Centre 990: Eclgical and Sciecnmic Functins f Trpical Lwland Rainfrest Transfrmatin Systems (Sumatra, Indnesia) BExIS 2 (DFG-Prject): generic pen surce infrmatin system fr bidiversity data (funded until 2017; live dem; dwnlad BExIS) Instances: idiv (DFG), AquaDiva (DFG), UFZ

6 BExIS: basic features Features Access: free, as generic tl nt restricted t bidiversity data! Imprt f structured (spreadsheet-based) and unstructured data (e.g. images) Internal table-t-database cnversin Data type cnsistency check Metadata (imprt structures as xsd = xml schema definitin) Exprt (csv, xlsx) Administratin f admissin rights Mdular architecture (data planning, data cllectin, data disseminatin, data discvery, system administratin)

7 BExIS: basic advantages Ideal fr (large) prjects and grups all data including metadata are at ne place (data base mangement in backgrund) Web interface Individual data access management Data base: even search within primary data Ingests all kind f data Dataset versining Clse interactin users develpers in prject runtime User and develper cnference June 9-10, 2016 in Jena (Germany)

8 Fr IT administratrs: Running BExIS Installatin requirements PstgreSQL r IBM DB2 Express-C.NET Framewrk Internet Infrmatin Service (IIS; Micrsft web server) UFZ instance Virtual machine in DMZ DeMilitarized Zne; utside firewall Cnnected t LDAP (Lightweight Directry Access Prtcl) easy lgin fr UFZ users accessible as web applicatin within intranet UFZ (bexis.ufz.de) https access fr utside wrld pssible

9 Getting rganized by sftware DATA STRUCTURE (table f variables, each variable characterized by data type, unit, attribute) Data attributes (area, time, quantity, relatinship...) Variable: Bimass quantity has attribute Data units (nne, dimensins [m, h, kg, rati]...) kg has unit Data types (string, number, date,...) number

10 Data structure dwnlad Excel template

11 Excel template (xlsm) Template with cmplete data structure entries and makr running in the backgrund

12 Excel template (xlsm) Cpy & paste yur data in the template Data type cnsistency check example: test is n number and thus indicated by the red cell

13 Wrkflw fr bidiversity data at UFZ Imprt Technical Quality Cntrl Spreadsheet data Exprt BExIS BExIS Search (terms; semantic) Cntent Quality Cntrl UFZ Data Management Prtal Archive cmpnent (file based) UFZ Data Research Prtal ( landing page ) DOI

14 Manage users grups features data permissins

15 Larger cntext: German Federatin fr Bilgical Data (GFBi; DFG prject; BExIS is a cmpnent) sustainable, service riented, natinal data infrastructure facilitating data sharing and stimulating data intensive science in the fields f bilgical and envirnmental research Data fcus: genme data, eclgical and envirnmental data, cllectin related data Cverage: full life cycle f research data field r real time data acquisitin lng term archiving publicatin re-analysis and re-use

16 Frm data management t DOI fr data sets DOI = Digital Object Identifier BExIS imprtant step twards DOI quality f data sets Why DOI fr data sets? Credits t data prducers / wners Persistent identifiers, persistant strage Standardised metadata Increasing requirement frm publishers Easy access via individual landing page (url) fr each data set

17 Frm data management t DOI fr data sets One ptin PANGAEA ( publicatin agent fr dataset DOI) Features f PANGAEA Jira ticket system fr data submissin and dcumentatin Editrial system (4D client) Structured data splitted t database Ontlgies behind Database + Ontlgy = Data warehuse essential fr reuse and new cmbinatin f related datasets! Link t exemplary landing page in PANGAEA