Enabling Precise Identification and Citability of Dynamic Data: Recommendations of the RDA Working Group on Data Citation

Enabling Precise Identification and
Citability of Dynamic Data:
Recommendations of the
RDA Working Group on Data Citation
Andreas Rauber
Vienna University of Technology
Favoritenstr. 9-11/188
1040 Vienna, Austria
rauber@ifs.tuwien.ac.at
http://ww.ifs.tuwien.ac.at/~andi

Motivation
 Research data is fundamental for science
- Results are based on data
- Data serves as input for workflows and experiments
- Data is the source for graphs and visualisations in publications
 Data is needed for Reproducibility
- Repeat experiments
- Verify / compare results
 Need to provide specific data set
- Service for data repositories
 Put data in data repository,
Assign PID (DOI, Ark, URI, …)
Make is accessible
 done?
Source: open.wien.gv.at
https://commons.wikimedia.org/w/index.php?curid=30978545

Identification of Dynamic Data
 Usually, datasets have to be static
- Fixed set of data, no changes:
no corrections to errors, no new data being added
 But: (research) data is dynamic
- Adding new data, correcting errors, enhancing data quality, …
- Changes sometimes highly dynamic, at irregular intervals
 Current approaches
- Identifying entire data stream, without any versioning
- Using “accessed at” date
- “Artificial” versioning by identifying batches of data (e.g.
annual), aggregating changes into releases (time-delayed!)
 Would like to identify precisely the data
as it existed at a specific point in time

Granularity of Subsets
 What about the granularity of data to be identified?
- Enormous amounts of CSV data
- Researchers use specific subsets of data
- Need to identify precisely the subset used
 Current approaches
- Storing a copy of subset as used in study -> scalability
- Citing entire dataset, providing textual description of subset
-> imprecise (ambiguity)
- Storing list of record identifiers in subset -> scalability,
not for arbitrary subsets (e.g. when not entire record selected)
 Would like to be able to identify precisely the
subset of (dynamic) data used in a process

What we do NOT want…
 Common approaches to data management…
(from PhD Comics: A Story Told in File Names, 28.5.2010)
Source: http://www.phdcomics.com/comics.php?f=1323

 Research Data Alliance
 WG on Data Citation:
Making Dynamic Data Citeable
 March 2014 – September 2015
- Concentrating on the problems of
large, dynamic (changing) datasets
 Final version presented Sep 2015
at P7 in Paris, France
 Endorsed September 2016
at P8 in Denver, CO
https://www.rd-alliance.org/groups/data-citation-wg.html
RDA WG Data Citation

RDA WGDC - Solution
 We have
‒ Data & some means of access („query“)

RDA WGDC - Solution
 We have
 Make
‒ Data: time-stamped and versioned
‒ Query: timestamped

RDA WGDC - Solution
 We have
 Make
‒ Data: time-stamped and versioned
‒ Query: timestamped
 Data Citation:
‒ Store query
‒ Assign the PID to the timestamped query
(which, dynamically, leads to the data)
 Access:
Re-execute query on versioned data according to timestamp
 Dynamic Data Citation:
Dynamic data & dynamic citation of data

Data Citation – Deployment
 Researcher uses workbench to identify subset of data
 Upon executing selection („download“) user gets
− Data (package, access API, …)
− PID (e.g. DOI) (Query is time-stamped and stored)
− Hash value computed over the data for local storage
− Recommended citation text (e.g. BibTeX)
 PID resolves to landing page
− Provides detailed metadata, link to parent data set, subset,…
− Option to retrieve original data OR current version OR changes
 Upon activating PID associated with a data citation
− Query is re-executed against time-stamped and versioned DB
− Results as above are returned
 Query store aggregates data usage

Note: query string provides excellentNote: query string provides excellent
provenance information on the data set!provenance information on the data set!

This is an important advantage overThis is an important advantage over
traditional approaches relying on, e.g.traditional approaches relying on, e.g.
storing a list of identifiers/DB dump!!!storing a list of identifiers/DB dump!!!

This is an important advantage overThis is an important advantage over
traditional approaches relying on, e.g.traditional approaches relying on, e.g.
storing a list of identifiers/DB dump!!!storing a list of identifiers/DB dump!!!
Identify which parts of the data are used.Identify which parts of the data are used.
If data changes, identify which queriesIf data changes, identify which queries
(studies) are affected(studies) are affected

Data Citation – Output
 14 Recommendations
grouped into 4 phases:
- Preparing data and query store
- Persistently identifying specific data sets
- Resolving PIDs
- Upon modifications to the data
infrastructure
 2-page flyer
https://
rd-alliance.org/recommendations-working-group-data-citation-revision-oct-20-2015.htm
 More detailed report: IEEE TCDL 2016
http://www.ieee-tcdl.org/Bulletin/v12n1/papers/IEEE-
TCDL-DC-2016_paper_1.pdf

Data Citation – Recommendations
Preparing Data & Query Store
- R1 – Data Versioning
- R2 – Timestamping
- R3 – Query Store
When Data should be persisted
- R4 – Query Uniqueness
- R5 – Stable Sorting
- R6 – Result Set Verification
- R7 – Query Timestamping
- R8 – Query PID
- R9 – Store Query
- R10 – Citation Text
When Resolving a PID
- R11 – Landing Page
- R12 – Machine Actionability
Upon Modifications to the
Data Infrastructure
- R13 – Technology Migration
- R14 – Migration Verification

A) Preparing the Data and the Query Store
R1 – Data Versioning: Apply versioning to ensure earlier
states of data sets the data can be retrieved
R2 – Timestamping: Ensure that operations on data are
timestamped, i.e. any additions, deletions are marked with a
timestamp
R3 – Query Store: Provide means to store the queries and
metadata to re-execute them in the future

A) Preparing the Data and the Query Store
R1 – Data Versioning: Apply versioning to ensure earlier
states of data sets the data can be retrieved
R2 – Timestamping: Ensure that operations on data are
timestamped, i.e. any additions, deletions are marked with a
timestamp
R3 – Query Store: Provide means to store the queries and
metadata to re-execute them in the future
NoteNote::
•R1 & R2R1 & R2 are already pretty much standard inare already pretty much standard in
many (RDBMS-) research databasesmany (RDBMS-) research databases
•Different ways to implementDifferent ways to implement
•A bit more challenging for some data typesA bit more challenging for some data types
(XML, LOD, …)(XML, LOD, …)
NoteNote::
•R3:R3: query store usually pretty small, even forquery store usually pretty small, even for
extremely high query volumesextremely high query volumes

B) Persistently Identify Specific Data sets (1/2)
When a data set should be persisted:
R4 – Query Uniqueness: Re-write the query to a normalized form so
that identical queries can be detected. Compute a checksum of the
normalized query to efficiently detect identical queries
R5 – Stable Sorting: Ensure an unambiguous sorting of the records
in the data set
R6 – Result Set Verification: Compute fixity information/checksum
of the query result set to enable verification of the correctness of a
result upon re-execution
R7 – Query Timestamping: Assign a timestamp to the query based
on the last update to the entire database (or the last update to the
selection of data affected by the query or the query execution time).
This allows retrieving the data as it existed at query time

B) Persistently Identify Specific Data sets (2/2)
When a data set should be persisted:
R8 – Query PID: Assign a new PID to the query if either the query
is new or if the result set returned from an earlier identical query is
different due to changes in the data. Otherwise, return the existing
PID
R9 – Store Query: Store query and metadata (e.g. PID, original
and normalized query, query & result set checksum, timestamp,
superset PID, data set description and other) in the query store
R10 – Citation Text: Provide citation text including the PID in the
format prevalent in the designated community to lower barrier for
citing data.

C) Resolving PIDs and Retrieving Data
R11 – Landing Page: Make the PIDs resolve to a human readable
landing page that provides the data (via query re-execution) and
metadata, including a link to the superset
(PID of the data source) and citation text snippet
R12 – Machine Actionability: Provide an API / machine actionable
landing page to access metadata and data via query re-execution

D) Upon Modifications to the Data Infrastructure
R13 – Technology Migration: When data is migrated to a new
representation (e.g. new database system, a new schema or a
completely different technology), migrate also the queries and
associated checksums
R14 – Migration Verification: Verify successful data and query
migration, ensuring that queries can be re-executed correctly

Pilot Adopters
 Several adopters
- Different types of data, different settings, …
- CSV & SQL reference implementation (SBA/TUW)
 Pilots:
- Biomedical BigData Sharing, Electronic Health Records
(Center for Biomedical Informatics, Washington Univ. in St. Louis)
- Marine Research Data
Biological & Chemical Oceanography Data Management Office
(BCO-DMO)
- Vermont Monitoring Cooperative: Forest Ecosystem Monitoring
- ARGO Boy Network, British Oceanographic Data Centre (BODC)
- Virtual Atomic and Molecular Data Centre (VAMDC)
- UK Riverflow Riverflow Archive, Centre for Ecology and Hydrology

WG Data Citation Pilot
CBMI @ WUSTL
Cynthia Hudson Vitale, Leslie McIntosh,
Snehil Gupta
Washington University in St.Luis

Biomedical Adoption Project Goals

RDA-MacArthur Grant Focus
Researchers
Data Broker

R1 and R2 Implementation
PostgreSQL Extension
“temporal_tables”
c1 c2 c3
RDC.table
sys_period
c1 c2 c3 sys_period
RDC.hist_table*
*stores history of data
changes
1
2
3
triggers

Return on Investment (ROI) -
Estimated
 20 hours to complete 1 study
 $150/hr (unsubsidized)
 $3000 per study
 115 research studies per year
 14 replication studies

Adoption of Data Citation Outcomes
by BCO-DMO
Cynthia Chandler, Adam Shepherd

 An existing repository (http://bco-dmo.org/)
 Marine research data curation since 2006
 Faced with new challenges, but no new funding
 e.g. data publication practices to support citation
 Used the outcomes from the RDA Data Citation
Working Group to improve data publication and citation
services
A story of success enabled by RDA

Adoption of Data Citation Outputs
 Evaluation
- Evaluate recommendations (done December 2015)
- Try implementation in existing BCO-DMO architecture
(work began 4 April 2016)
 Trial
- BCO-DMO: R1-11 fit well with current architecture; R12 doable;
test as part of DataONE node membership; R13-14 are
consistent with Linked Data approach to data publication and
sharing
 Timeline:
- Redesign/protoype completed by 1 June 2016
- New citation recommendation by 1 Sep 2016
- Report out at RDA P8 (Denver, CO) September 2016
- Final report by 1 December 2016

Vermont Monitoring Cooperative
James Duncan, Jennifer Pontius
VMC

Ecosystem Monitoring
Collaborator Network
Data Archive, Access and
Integration

USERWORKFLOWTO DATE
 Modify a dataset
 changes tracked
 original data table unchanged
 Commit to version, assign name
 computes result hash (table pkid, col
names, first col data) and query hash
 updates data table to new state
 formalizes version
 Restore previous version
 creates new version table from current
data table state,
 walks it back using stored SQL.
 Garbage collected after a period of time

UK Riverflow Archive
Matthew Fry
mfry@ceh.ac.uk

Global Water Information Interest Group meeting
RDA 8th
Plenary, 15th
September 2016, Denver
UK National River Flow Archive
• ORACLE Relational database
• Time series and metadata tables
• ~20M daily flow records, + monthly / daily catchment rainfall series
• Metadata (station history, owners, catchment soils / geology, etc.)
• Total size of ~5GB
• Time series tables automatically audited,
• But reconstruction is complex
• Users generally download simple files
• But public API is in development / R-NRFA package is out there
• Fortunately all access is via single codeset

Global Water Information Interest Group meeting
RDA 8th
Plenary, 15th
September 2016, Denver
Versioning / citation solution
• Automated archiving of entire database – version controlled scripts
defining tables, creating / populating archived tables (largely complete)
• Fits in with data workflow – public / dev versions – this only works because
we have irregular / occasional updates
• Simplification of the data model (complete)
• API development (being undertaken independently of dynamic citation
requirements):
• allows subsetting of dataset in a number of ways – initially simply
• need to implement versioning (started) to ensure will cope with changes to data
structures
• Fit to dynamic data citation recommendations?
• Largely
• Need to address mechanism for users to request / create citable version of a query
• Resource required: estimated ~2 person months

Reference Implementation for
CSV Data (and SQL)
Stefan Pröll, SBA

38
CSV/SQL Reference Implementation 1
 Reference Implementation available on Github
https://github.com/datascience/RDA-WGDC-CSV-Data-Citation-Prototype
 Upload interface -->Upload CSV files
 Migrate CSV file into RDBMS
−Generate table structure, identify primary key
−Add metadata columns for versioning (transparent)
−Add indices (transparent)
 Dynamic data: upload new version of file
−Versioned update / delete existing records in RDBMS
 Access interface
−Track subset creation
−Store queries -> PID + Landing Page
Barrymieny

39
CSV/Git Reference Implementation 2
 Based on Git only (no SQL database)
 Upload CSV files to Git repository
 SQL-style queries operate on CSV file via API
 Data versioning with Git
 Store scripts versioned as well
 Make subset creation reproducible

40
CSV/Git Reference Implementation 2
 Stefan Pröll, Christoph Meixner, Andreas Rauber
Precise Data Identification Services for Long Tail Research Data.
Proceedings of the intl. Conference on Preservation of Digital Objects
(iPRES2016), Oct. 3-6 2016, Bern, Switzerland.
 Source at Github:
https://github.com/datascience/
RDA-WGDC-CSV-Data-Citation-Prototype
 Videos:
 Login: https://youtu.be/EnraIwbQfM0
 Upload: https://youtu.be/xJruifX9E2U
 Subset: https://www.youtube.com/watch?v=it4sC5vYiZQ
 Resolver: https://youtu.be/FHsvjsUMiiY
 Update: https://youtu.be/cMZ0xoZHUyI

Benefits
 Retrieval of precise subset with low storage overhead
 Subset as cited or as it is now (including e.g. corrections)
 Query provides provenance information
 Query store supports analysis of data usage
 Checksums support verification
 Same principles applicable across all settings
- Small and large data
- Static and dynamic data
- Different data representations (RDBMS, CSV, XML, LOD, …)
 Would work also for more sophisticated/general
transformations on data beyond select/project

Thanks!
https://rd-alliance.org/working-groups/data-citation-wg.html
Thank you!

 RDA recommendations implemented in data infrastructures
 Required adaptions
- Introduce versioning, if not already in place
- Capture sub-setting process (queries)
- Implement dedicated query store to
store queries
- A bit of additional functionality
(query re-writing, hash functions, …)
 Done! ?
- “Big data”, database driven
- Well-defined interfaces
- Trained experts available
- “Complex, only for professional research infrastructures” ?
Large Scale Research Settings

Long Tail Research Data
Big data,
well organized,
often used and cited
Less well organized,
non-standardised
no dedicated infrastructure
“Dark data”
Amount of data sets
Data set size
[1] Heidorn, P. Bryan. "Shedding light on the dark data in the long tail of science." Library Trends 57.2 (2008): 280-299.

Prototype Implementations
 Solution for small-scale data
- CSV files, no “expensive” infrastructure, low overhead
2 Reference implementations :
 Git based Prototypes: widely used versioning system
- A) Using separate folders
- B) Using branches
 MySQL based Prototype:
- C) Migrates CSV data into relational database
 Data backend responsible for versioning data sets
 Subsets are created with scripts or queries
via API or Web Interface
 Transparent to user: always CSV

CSV Reference Implementation 2
Git Implementation 1
Upload CSV files to Git repository (versioning)
Subsets created via scripting language (e.g. R)
 Select rows/columns, sort, returns CSV + metadata file
 Metdata file with script parameters stored in Git
 (Scripts stored in Git as well)
PID assigned to metadata file
 Use Git to retrieve proper data set version
and re-execute script on retrieved file

Git-based Prototype
Git Implementation 2
Addresses issues
- common commit history, branching data
Using Git branching model:
Orphaned branches for queries and data
- Keeps commit history clean
- Allows merging of data files
Web interface for queries (CSV2JDBC)
Use commit hash for identification
- Assigned PID hashed with SHA1
- Use hash of PID as filename (ensure permissible characters)

Git-based Prototype
Step 1: Select a CSV
file in the repository
Step 2: Create a
subset with a SQL
query (on CSV data)
Step 3: Store the query
script and metadata
Step 4: Re-Execute!
 Prototype: https://github.com/Mercynary/recitable

MySQL-based Prototype
MySQL Prototype
Data upload
- User uploads a CSV file into the system
Data migration from CSV file into RDBMS
- Generate table structure
- Add metadata columns (versioning)
- Add indices (performance)
Dynamic data
- Insert, update and delete records
- Events are recorded with a timestamp
Subset creation
- User selects columns, filters and sorts records in web interface
- System traces the selection process
- Exports CSV
Barrymieny

MySQL-based Prototype
‒ https://github.com/datascience/RDA-WGDC-CSV-Data-Citation-Prototype
 Videos:
‒ Login: https://youtu.be/EnraIwbQfM0
‒ Upload: https://youtu.be/xJruifX9E2U
‒ Subset: https://www.youtube.com/watch?v=it4sC5vYiZQ
‒ Resolver: https://youtu.be/FHsvjsUMiiY
‒ Update: https://youtu.be/cMZ0xoZHUyI

CSV Reference Implementation 2
 Stefan Pröll, Christoph Meixner, Andreas Rauber
Precise Data Identification Services for Long Tail Research Data.
Proceedings of the intl. Conference on Preservation of Digital Objects
(iPRES2016), Oct. 3-6 2016, Bern, Switzerland.
https://github.com/datascience/
RDA-WGDC-CSV-Data-Citation-Prototype
 Videos:
 Login: https://youtu.be/EnraIwbQfM0
 Upload: https://youtu.be/xJruifX9E2U
 Subset: https://www.youtube.com/watch?v=it4sC5vYiZQ
 Resolver: https://youtu.be/FHsvjsUMiiY
 Update: https://youtu.be/cMZ0xoZHUyI

Moving Biomedical Big Data
Sharing Forward
An adoption of the RDA Data Citation of Evolving Data
Recommendation to Electronic Health Records
Leslie McIntosh, PHD, MPH RDA P8
Cynthia Hudson Vitale, MA Denver, USA September
2016
@mcintold
@cynhudson

 Director, Center
for Biomedical
Informatics
 Data Services
Coordinator

Leslie McIntosh, PHD,
MPH


Cynthia Hudson Vitale,
MA


BDaaS
Biomedical Data as a
Service
Researchers
Data
Broker
i2b2
Application
Biomedical
Data
Repository

Move some of the responsibility of reproducibility
Biomedical
Researcher
Biomedical
Pipeline

Biomedical Adoption Project Goals
Implement RDA Data Citation WG recommendation to
local Washington U i2b2
Engage other i2b2 community adoptees
Contribute source code back to i2b2 community

RDA Data Citation WG
Recommendations
R1: Data Versioning
R2: Data Timestamping
R3, R9: Query Store
R7: Query Timestamping
R8: Query PID
R10: Query Citation

Internal Implementation
Requirements
 Scalable
 Available for PostgreSQL
 Actively supported
 Easy to maintain
 Easy for data brokers to use

ETL Incrementals
Source Data
Update?
… sys_period
2016-9-9 00:00,
NULL
RDC.table
Old Data
… sys_period
2016-9-8 00:00,
2016-9-9 00:00
RDC.hist_table
Insert?
… sys_period
2016-9-9 00:00,
NULL
RDC.table

R3, R7, R8, R9, and R10
Implementation
PostgreSQL Extension
“temporal_tables”
1
RDC.table RDC.hist_table
RDC.table_with_history (view)
2 3
• functions
• triggers
• query audit
tables

Bonus Feature: Determine if Change
Occurred

Future Developments
 Develop a process for sharing Query PID with
researchers in an automated way
 Resolve Query PIDs to a landing page with
Query metadata
 Implement research reproducibility requirements
in other systems as possible

Obtained Outcomes
 Implemented WG recommendations
 Engaged with other i2b2 adoptees
(Harvard, Nationwide Children’s Hospital)

Dissemination
 Poster presentation (Harvard U, July 2016)
 Scientific manuscript based on our proof of concept to
AMIA TBI/CRI 2017 conference
 Sharing the code with the community

Funding Support
 MacArthur Foundation 2016 Adoption Seeds program Foundation
through a sub-contract with Research Data Alliance
 Washington University Institute of Clinical and Translational Sciences
 NIH CTSA Grant Number UL1TR000448 and UL1TR000448-09S1
 Siteman Cancer Center at Washington University
 NIH/NCI Grant P30 CA091842-14


Center for Biomedical Informatics @WUSTL
Teams for Reproducible Research

WashU CBMI Research Reproducibility
Resources

 BCO-DMO is a thematic, domain-specific repository
funded by NSF Ocean Sciences and Polar Programs
 BCO-DMO curated data are
- Served: http://bco-dmo.org (URLs, URIs)
- Published: at an Institutional Repository (CrossRef DOI)
http://dx.doi.org/10.1575/1912/4847
- Archived: at NCEI, a US National Data Center
http://data.nodc.noaa.gov/cgi-bin/iso?
id=gov.noaa.nodc:0078575
BCO-DMO Curated Data
for Linked Data URI: http://lod.bco-dmo.org/id/dataset/3046

BCO-DMO Dataset Landing Page (Mar ‘16)

Initial Architecture Design Considerations (Jan 2016)

Modified Architecture (March 2016)

BCO-DMO Data Publication System
Components
BCO-DMO publishes data to WHOAS and a DOI is assigned.
The BCO-DMO architecture now supports data versioning.

BCO-DMO Data Citation System Components

Enabling Precise Identification and Citability of Dynamic Data: Recommendations of the RDA Working Group on Data Citation

New Capabilities … BCO-DMO becoming a DataONE Member Node
https://search.dataone.org/

New Capabilities … BCO-DMO Data Set Citation

 To the Data Citation Working Group for their efforts
 RDA US for funding this adoption project
 TIMELINE:
- Redesign/protoype completed by 1 June 2016
- New citation recommendation by 1 Sep 2016
- Report out at RDA P8 (Denver, CO) September 2016
- Final report by 1 December 2016
Cyndy Chandler @cynDC42 @bcodmo
ORCID: 0000-0003-2129-1647 cchandler@whoi.edu
Thank you …

 Removed these to reduce talk to 10-15 minutes
EXTRA SLIDES

Adoption of Data Citation Outputs
 Evaluation
- Evaluate recommendations (done December 2015)
- Try implementation in existing BCO-DMO architecture
(work began 4 April 2016)
 Trial
- BCO-DMO: R1-11 fit well with current architecture; R12
doable; test as part of DataONE node membership; R13-
14 are consistent with Linked Data approach to data
publication and sharing
NOTE: adoption grant received from RDA US (April 2016)

RDA Data Citation (DC) of evolving
data
 DC goals: to create identification mechanisms that:
- allow us to identify and cite arbitrary views of data, from a single
record to an entire data set in a precise, machine-actionable
manner
- allow us to cite and retrieve that data as it existed at a certain
point in time, whether the database is static or highly dynamic
 DC outcomes: 14 recommendations and associated
documentation
- ensuring that data are stored in a versioned and timestamped
manner
- identifying data sets by storing and assigning persistent
identifiers (PIDs) to timestamped queries that can be re-
executed against the timestamped data store

RDA Data Citation WG
Recommendations
»» Data Versioning: For retrieving earlier
states of datasets the data need to be
versioned. Markers shall indicate inserts,
updates and deletes of data in the database.
»» Data Timestamping: Ensure that operations
on data are timestamped, i.e. any additions,
deletions are marked with a
timestamp.
»» Data Identification: The data used shall be
identified via a PID pointing to a time-stamped
query, resolving to a landing page.
Oct 2015 version w/ 14 recommendations
DC WG chairs: Andreas Rauber, Ari Asmi,
Dieter van Uytvanck

procedure: when a BCO-DMO data set is updated …
A copy of the previous version is preserved
Request a DOI for the new version of data
Publish data, and create new landing page for new
version of data, with new DOI assigned
BCO-DMO database has links to all versions of the data
(archived and published)
Both archive and published dataset landing pages have
links back to best version of full dataset at BCO-DMO
BCO-DMO data set landing page displays links to all
archived and published versions
New capability
(implemented)

 Extended description of recommendations
 Altman and Crosas. 2013. “Evolution of Data Citation …”
 CODATA-ICSTI 2013. “Out of cite, out of mind”
 FORCE11 https://www.force11.org/about/mission-and-guiding-principles
 R. E. Duerr, et al. “On the utility of identification schemes for digital
earth science data”, ESI, 2011.
REFERENCES

Implementation of Dynamic Data Citation
James Duncan and Jennifer Pontius
9/16/2016
james.duncan@uvm.edu, www.uvm.edu/vmc

Many Disciplines, Many
Contributors
VMC houses any data related to forest
ecosystem condition, regardless of affiliation or
discipline

Why We Need It
 Continually evolving
datasets
 Some errors not caught
till next field season
 Frequent reporting and
publishing

Dynamic Data Citation –
Features Needed
 Light footprint on database resources
 Works on top of existing catalog and metadata
 Works in an institutionally managed PHP/MySQL
environment
 User-driven control of what quantity of change
constitutes a version
 Integration with management portal
 Track granular changes in data

User Workflow to Date
 Modify a dataset
- changes tracked
- original data table unchanged
 Commit to version, assign name
- computes result hash (table pkid, col
names, first col data) and query hash
- updates data table to new state
- formalizes version
 Restore previous version
- creates new version table from current
data table state,
- walks it back using stored SQL.
- Garbage collected after a period of time

User Workflow, still to come
 Web-based data editing
validation
 DOI minting integration
 Public display
 Subsetting workflow
 Other methods of data
modification?
 Upgrade to rest of
system
V1.1
V1.2
V1.3 Query 1
Unsaved
DOI:
DOI:
DOI?

Technical Details
Version
PID
Datase
t ID
Version
Name
Version
ID
Person
ID
Query
Hash
Result
Hash
Timesta
mp
23456 3525 Version
1.5
3 …. …. ….
23574 3525 Unsaved -1 …. NULL ….
Step ID Version
PID
Forward Backward Order
983245 23574 DELETE
FROM…
INSERT INTO… 1
983245 23574 UPDATE
SET
site=“Winhall
”…
UPDATE SET
site=“Lye
Brook”…
2
Version Info Table
Step Tracking Table (Child of Version Info)

Implementation Challenges and
Questions
Challenges
Large updates
Re-creation of past versions, in terms of garbage
collection and storage
Questions
Query uniqueness checking and query normalization
Efficient but effective results hashing strategies
Linear progression of data, versus branching network

Acknowledgments
 Adoption seed funding - MacArthur Foundation and the
Research Data Alliance
 The US Forest Service State and Private Forestry
program for core operational funding of the VMC
 Fran Berman, Yolanda Meleco and the other adopters
who have been sharing their experiences.
 All the VMC cooperators that contribute

ARGO
Justin Buck, Helen Glaves
BODC

WG Data Citation: Adoption
meeting
Argo DOI pilot
Justin Buck, National Oceanography Centre (UK),
juck@bodc.ac.uk
Thierry Carval, Ifremer (France), thierry.carval@ofremer.fr
Thomas Loubrieu, Ifremer (France), thomas.loubrieu@ifremer.fr
Frederic Merceur, Ifremer (France), frederic.merceur@ifremer.fr
RDA P8 2016, Denver, 16th
September 2016

300+ citations per
year
How to cite Argo data at a given point in time?
Possible with a single DOI?

Argo data system (simplified)
Raw
data
Data Assembly Centres (DAC)
(national level, 10 of, RT processing and QC) GTS
(+GTSPP
archive)
Global data assembly Centres (GDAC)
(2 of, mirrored, ftp access,
repository of NetCDF files, no
version control, latest version served)
Data users
Delayed mode
quality control

Key associated milestones
 2014 – Introduction of dynamic data into the DataCite
metadata schema
- https://schema.datacite.org/
- Snapshots were used as an interim solution for Argo
 2015 – RDA recommendations on evolving data:
- https://rd-alliance.org/system/files/RDA-DC-
Recommendations_151020.pdf
- Legacy GDAC architecture does not permit full implementation

How to apply a DOI for Argo
Obs time
Statetime
++
+
++
+++ +
+
++
+
+
+
++
+
+ + +
+
+
++
+++
Obs time
Statetime
++
+
++
+++ +
+
++
+
+
+
++
+
+ + +
+
+
++
+++
Obs time
Statetime
++
+
++
+++ +
+
++
+
+
+
++
+
+ + +
+
+
++
+++
Archive (collection of snapshots/granules)
To cite a particular snapshot one can potentially cite a time slice of an archive i.e. the
snapshot at a given point in time.

New single DOI
Argo (2000). Argo float data and metadata from Global Data Assembly
Centre (Argo GDAC). SEANOE. http://doi.org/10.17882/42182

# key used to identify snapshot

# key used to identify snapshot
http://www.seanoe.org/data/00311/42182/#45420

Step towards RDA recommendation
Archive snapshots enables R1 and R2 at monthly granularity
R1 – Data Versioning R2 – Timestamping
Argo Pilot effectively uses predetermined referencing of snapshots removing
the need for requirements R3 to R7. # keys are PIDs for the snapshots and
have associated citation texts.
R3 – Query Store Facilities R4 – Query Uniqueness
R5 – Stable Sorting R6 – Result Set Verification
R7 – Query Timestamping R8 – Query PID
R9 – Store Query R10 – Automated Citation Texts
SEANOE landing page architecture means R11 and R12 effectively met
R11 – Landing Page R12 – Machine Actionability
Final two requirements untested at this stage
R13 – Technology Migration R14 – Migration Verification

Summary
 There is now a single DOI for Argo
- Takes account of legacy GDAC architecture
- Monthly temporal granularity
- Enables both reproducible research and simplifies the tracking
of citations
- ‘#’ rather than ‘?’ in identifier takes account of current DOI
resolution architecture
 Extensible to other observing systems such as
OceanSITES and EGO
 The concept allows for different subsets of Argo data
e.g. ocean basins, Bio-Argo data

Progress on Data Citation within
VAMDC
C.M. Zwölf and VAMDC Consortium
carlo-maria.zwolf@obspm.fr

From RDA Data Citation
Recommendations to new paradigms
for citing data from VAMDC
C.M. Zwölf and VAMDC consortium
RDA 8th
Plenary - Denver

VAMDC
Single and
unique
access to
heterogeneou
s A+M
Databases
VAMDC
Single and
unique
access to
heterogeneou
s A+M
Databases
Federates 29 heterogeneous databases
http://portal.vamdc.org/
The “V” of VAMDC stands for Virtual in the
sense that the e-infrastructure does not
contain data. The infrastructure is a
wrapping for exposing in a unified way a set
of heterogeneous databases.
The consortium is politically organized
around a Memorandum of understanding
(15 international members have signed the
MoU, 1 November 2014)
High quality scientific data come from
different Physical/Chemical Communities
Provides data producers with a large
dissemination platform
Remove bottleneck between data-
producers and wide body of users
The Virtual Atomic and Molecular Data Centre

Existing
Independent
A+M
database
Existing
Independent
A+M
database
The VAMDC infrastructure technical architecture

VAMDC wrapping
layer  VAMDC
Node
VAMDC wrapping
layer  VAMDC
Node
Existing
Independent
A+M
database
Existing
Independent
A+M
database
Resource
registered
into
Standard LayerStandard Layer
Accept queries submitted in
standard grammar
standard grammar
Results formatted into
standard XML file (XSAMS)
Registry
Layer
Registry
Layer

VAMDC wrapping
layer  VAMDC
Node
VAMDC wrapping
layer  VAMDC
Node
Existing
Independent
A+M
database
Existing
Independent
A+M
database
Resource
registered
into
Unique
A+M query
Unique
A+M query
Asks for available
resources
VAMDC
Clients
(dispatch
query on all
the
registered
resources)
•Portal
•SpecView
•SpectCol
VAMDC
Clients
(dispatch
query on all
the
registered
resources)
•Portal
•SpecView
•SpectCol
Set of
standard
files
Set of
standard
files
standard grammar
standard grammar
Registry
Layer
Registry
Layer

VAMDC wrapping
layer  VAMDC
Node
VAMDC wrapping
layer  VAMDC
Node
Existing
Independent
A+M
database
Existing
Independent
A+M
database
Resource
registered
into
Unique
A+M query
Unique
A+M query
Asks for available
resources
VAMDC
Clients
(dispatch
query on all
the
registered
resources)
•Portal
•SpecView
•SpectCol
VAMDC
Clients
(dispatch
query on all
the
registered
resources)
•Portal
•SpecView
•SpectCol
Set of
standard
files
Set of
standard
files
standard grammar
standard grammar
Registry
Layer
Registry
Layer
• VAMDC is agnostic about the local data storage strategy on each node.
• Each node implements the access/query/result protocols.
• There is no central management system.
• Decisions about technical evolutions are made by consensus in Consortium.
 It is both technical and political challenging to implement the WG recommendations.

Let us implement the recommendation!!
Tagging and versioning dataTagging and versioning data
The problem is more anthropological than technical…The problem is more anthropological than technical…
What does it really mean
data citation?
data citation?

We see technically how to do thatWe see technically how to do that
But each data provider defines differently what a
dataset is.
dataset is.
Naturally it is the dataset (A+M data have no
meaning outside this given context)
Ok, but What is the data granularity for tagging?Ok, but What is the data granularity for tagging?
data citation?
data citation?

We see technically how to do thatWe see technically how to do that
dataset is.
dataset is.
Ok, but What is the data granularity for tagging?Ok, but What is the data granularity for tagging?
data citation?
data citation?
Everyone knows what it is!Everyone knows what it is!
Yes, but everyone has its own definitionYes, but everyone has its own definition
RDA cite databases record or output files.
(an extracted data file may have an H-factor)
RDA cite databases record or output files.
(an extracted data file may have an H-factor)
VAMDC cite all the papers used for compiling
the content of a given output file.
VAMDC cite all the papers used for compiling
the content of a given output file.

Tagging versions of dataTagging versions of data
Implementation will be an overlay to the standard / output layer, thus
independent from any specific data-node
Twolayers
mechanisms
Twolayers
mechanisms
1  Fine grained granularity:
Evolution of XSAMS output
standard for tracking data
modifications
modifications
2  Coarse grained
granularity:
At each data modification to a
given data node, the version
of the Data-Node changes
granularity:
With the second mechanism we know that
something changed : in other words, we
know that the result of an identical query
may be different from one version to the
other. The detail of which data changed is
accessible using the first mechanisms.

Query StoreQuery StoreTagging versions of dataTagging versions of data
Twolayers
mechanisms
Twolayers
mechanisms
modifications
modifications
granularity:
granularity:
Is built over the versioning of DataIs built over the versioning of Data
Is plugged over the existing
VAMDC data-extraction
mechanisms.
Is plugged over the existing
VAMDC data-extraction
mechanisms.
Due to the distributed VAMDC
architecture, the Query Store
architecture is similar to a log-service.
Due to the distributed VAMDC
architecture, the Query Store
architecture is similar to a log-service.

Data-Versioning: overview of the fine grained
mechanisms
OutputXSAMSfile
Radiative process
1
Radiative process
1
Radiative process
2
Radiative process
2
We adopted a change of paradigm (weak structuration):
Radiative process
n
Radiative process
n
…
Collisional process 1Collisional process 1
Collisional process
m
Collisional process
m
…
Energy State 1Energy State 1
Energy State pEnergy State p
……
Element 1Element 1
Element 2Element 2
Element qElement q

OutputXSAMSfile
Radiative process
1
Radiative process
1
Radiative process
2
Radiative process
2
Radiative process
n
Radiative process
n
…
Collisional process
m
Collisional process
m
…
……
Element 1Element 1
Element 2Element 2
Element qElement q
Version 1
(tagged according
to infrastructure
state & updates)
Version 2
(tagged according
to infrastructure
state & updates)
Data-Versioning: overview of the fine grained mechanisms

OutputXSAMSfile
Radiative process
1
Radiative process
1
Radiative process
2
Radiative process
2
Radiative process
n
Radiative process
n
…
Collisional process
m
Collisional process
m
…
……
Element 1Element 1
Element 2Element 2
Element qElement q
Version 1
(tagged according
to infrastructure
state & updates)
Version 2
(tagged according
to infrastructure
state & updates)
mechanisms

This approach has several advantages:
•It solves the data tagging granularity problem
•It is independent from what is considered a dataset
•The new files are compliant with old libraries & processing programs
• We add a new feature, an overlay to the existing structure
• We induce a structuration, without changing the structure (weak
structuration)
mechanisms

We adopted a change of paradigms:
This approach has several advantages:
•It solves the data tagging granularity problem
•It is independent from what is considered a dataset
•The new files are compliant with old libraries & processing programs
• We add a new feature, an overlay to the existing structure
• We induce a structuration, without changing the structure (weak
structuration)
Technical details described in
New model for datasets citation and extraction reproducibility in VAMDC,
C.M. Zwölf, N. Moreau, M.-L. Dubernet,
In press J. Mol. Spectrosc. (2016),
http://dx.doi.org/10.1016/j.jms.2016.04.009
Arxiv version: https://arxiv.org/abs/1606.00405
Technical details described in
New model for datasets citation and extraction reproducibility in VAMDC,
C.M. Zwölf, N. Moreau, M.-L. Dubernet,
In press J. Mol. Spectrosc. (2016),
http://dx.doi.org/10.1016/j.jms.2016.04.009
Arxiv version: https://arxiv.org/abs/1606.00405
Data-Versioning: overview of the fine grained mechanisms

Let us focus on the query store:
The difficulty we have to cope with:
•Handle a query store in a distributed environment (RDA did not design
it for these configurations).
•Integrate the query store with the existing VAMDC infrastructure.

The implementation of the query store is the goal of a joint
collaboration between VAMDC and RDA-Europe.
•Development started during spring 2016.
•Final product released during 2017.
The implementation of the query store is the goal of a joint

The implementation of the query store is the goal of a jointly
The implementation of the query store is the goal of a jointly
Collaboration with Elsevier for embedding the VAMDC query store into
the pages displaying the digital version of papers.
Designing technical solution for
•Paper / data linking at the paper submission (for authors)
•Paper / data linking at the paper display (for readers)
Collaboration with Elsevier for embedding the VAMDC query store into
the pages displaying the digital version of papers.
Designing technical solution for
•Paper / data linking at the paper submission (for authors)
•Paper / data linking at the paper display (for readers)

Data extraction procedure
VAMDC
portal
(query
interface)
VAMDC
portal
(query
interface)
VAMDC
infrastructur
e
VAMDC
infrastructur
e
Query
VAMD portal
(result part)
VAMD portal
(result part)
Computed
response
Access to the
output data file
Access to the
output data file
Digital Unique
Identifier
associated to
the current
extraction
Digital Unique
Identifier
associated to
the current
extraction
Submitting
query
Sketching the functioning – From the final-user point of view:

VAMDC
portal
(query
interface)
VAMDC
portal
(query
interface)
VAMDC
infrastructur
e
VAMDC
infrastructur
e
Query
VAMD portal
(result part)
VAMD portal
(result part)
Computed
response
Access to the
output data file
Access to the
output data file
Digital Unique
Identifier
associated to
the current
extraction
Digital Unique
Identifier
associated to
the current
extraction
Submitting
query
Resolves
Landing
Page
Landing
Page
The original queryThe original query
Date & time where query was
processed
processed
Version of the infrastructure when
the query was processed
List of publications needed for
answering the query
answering the query
When supported (by the VAMDC
federated DB): retrieve the output
data-file as it was computed
(query re-execution)
Query
Metadata
Query
Metadata
QueryStore

VAMDC
portal
(query
interface)
VAMDC
portal
(query
interface)
VAMDC
infrastructur
e
VAMDC
infrastructur
e
Query
VAMD portal
(result part)
VAMD portal
(result part)
Computed
response
Access to the
output data file
Access to the
output data file
Digital Unique
Identifier
associated to
the current
extraction
Digital Unique
Identifier
associated to
the current
extraction
Submitting
query
Resolves
Landing
Page
Landing
Page
processed
processed
answering the query
answering the query
Query
Metadata
Query
Metadata
QueryStore
Manage queries
(with
authorisation/auth
entication)
Manage queries
(with
authorisation/auth
entication)
Group arbitrary set
of queries (with
related DUI) and
assign them a DOI
to use in
publications
Group arbitrary set
of queries (with
related DUI) and
assign them a DOI
to use in
publications
UseDOIin
papers

VAMDC
portal
(query
interface)
VAMDC
portal
(query
interface)
VAMDC
infrastructur
e
VAMDC
infrastructur
e
Query
VAMD portal
(result part)
VAMD portal
(result part)
Computed
response
Access to the
output data file
Access to the
output data file
Digital Unique
Identifier
associated to
the current
extraction
Digital Unique
Identifier
associated to
the current
extraction
Submitting
query
Resolves
Landing
Page
Landing
Page
processed
processed
answering the query
answering the query
Query
Metadata
Query
Metadata
QueryStore
Manage queries
(with
authorisation/auth
entication)
Manage queries
(with
authorisation/auth
entication)
Group arbitrary set
of queries (with
related DUI) and
assign them a DOI
to use in
publications
Group arbitrary set
of queries (with
related DUI) and
assign them a DOI
to use in
publications
UseDOIin
papers
Editors may follow the citation pipeline :
credit delegation applies

Sketching the functioning – Technical internal point of view:
VAMDC
Node
VAMDC
Node
Query Store Listener
Service
Service
Notification
1  When a node receives a user query, it
notifies to the Listener Service the following
information:
•The identity of the user (optional)
•The used client software
•The identifier of the node receiving the query
•The version (with related timestamp) of the node receiving
the query
•The version of the output standard used by the node for
replying the results
•The query submitted by the user
•The link to the result data.
1  When a node receives a user query, it
notifies to the Listener Service the following
information:
•The identity of the user (optional)
•The used client software
•The identifier of the node receiving the query
•The version (with related timestamp) of the node receiving
the query
•The version of the output standard used by the node for
replying the results
•The query submitted by the user
•The link to the result data.

VAMDC
Node
VAMDC
Node
Service
Service
2  For each received notification,
the listener check if it exists an already
existing query:
•Having the same Query
•Having the same node version
•Submitted to the same node and having the
same node version
existing query:
same node version
Notification

VAMDC
Node
VAMDC
Node
Service
Service
existing query:
same node version
existing query:
same node version
• Provides the Query with a unique
time-stamped identifier
• Following the link, get data and
process them for extracting relevant
metadata (ex. Bibtex of references
used for compiling the output file)
• Store these relevant metadata
• If identity of user is provided, we
associate the user with the Query ID
• Provides the Query with a unique
time-stamped identifier
• Following the link, get data and
process them for extracting relevant
metadata (ex. Bibtex of references
used for compiling the output file)
• Store these relevant metadata
• If identity of user is provided, we
associate the user with the Query ID
Notification
• We get the already existing unique
identifier and (incrementally)
associate the new query timestamp
(and if provided the identifier of the
user) with the query Identifier
• We get the already existing unique
identifier and (incrementally)
associate the new query timestamp
(and if provided the identifier of the
user) with the query Identifier
existing
Notexisting

VAMDC
Node
VAMDC
Node
Service
Service
Notification
Remark on query uniqueness:
•The query language supported by the VAMDC infrastructure is VSS2 (VAMDC
SQL Subset 2,
http://vamdc.eu/documents/standards/queryLanguage/vss2.html).
•We are working on a specific VSS2 parser (based on Antlr) which should identify,
from queries expressed in different ways, the ones that are semantically identical
•We are designing this analyzer as an independent module, hoping to extend it to
all SQL.

Final remarks:
• Our aims:
• Provide the VAMDC infrastructure with an operational query store
• Share our experience with other data-providers
• Provide data-providers with a set of libraries/tools/methods for an easy
implementation of a query store.
• We will try to build a generic query store (i.e. using generic software
blocks)

 Curation and dissemination of regulatory
river flow data for research and other
access
 Data used for significant research
outputs, and a large number of citations
annually
 Updated annually but also regular
revision of entire flow series through time
(e.g. stations resurveyed)
 Internal auditing, but history is not
exposed to users

 ORACLE Relational database
 Time series and metadata tables
 ~20M daily flow records, + monthly / daily catchment
rainfall series
 Metadata (station history, owners, catchment soils /
geology, etc.)
 Total size of ~5GB
 Time series tables automatically audited,
- But reconstruction is complex
 Users generally download simple files
 But public API is in development / R-NRFA package is out
there
 Fortunately all access is via single codeset

Our data citation requirements
 Cannot currently cite whole dataset
 Allow citation a subset of the data, as it was at the time
 Fit with current workflow / update schedule, and
requirements for reproducibility
 Fit with current (file download) and future (API) user
practices
 Resilient to gradual or fundamental changes in
technologies used
 Allow tracking of citations in publications

Options for versioning / citation
 “Regulate” queries:
- limitations on service provided
 Enable any query to be timestamped / cited /
reproducible:
- does not readily allow verification (e.g. checksum) of queries
(R7), or storage of queries (R9)
 Manage which queries can be citable:
- limitation on publishing workflow?

Versioning / citation solution
 Automated archiving of entire database – version controlled scripts
defining tables, creating / populating archived tables (largely
complete)
 Fits in with data workflow – public / dev versions – this only works
because we have irregular / occasional updates
 Simplification of the data model (complete)
 API development (being undertaken independently of dynamic
citation requirements):
- allows subsetting of dataset in a number of ways – initially simply
- need to implement versioning (started) to ensure will cope with changes to
data structures
 Fit to dynamic data citation recommendations?
- Largely
- Need to address mechanism for users to request / create citable version of
a query
 Resource required: estimated ~2 person months

Enabling Precise Identification and Citability of Dynamic Data: Recommendations of the RDA Working Group on Data Citation

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Enabling Precise Identification and Citability of Dynamic Data: Recommendations of the RDA Working Group on Data Citation

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