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Preparation and planning for shared MPDL project "Scholarly Workbench for Astronomy"

Based on experiences and outcomes of German Virtual Observatory (GAVO)

Contacts@MPE: Jaiwon Kim, Gerard Lemson, Wolfgang Voges

Scenarios[edit]

Collaborative environment[edit]

Enable easy, wiki-like setup of collaborative environment for shared projects. Allow registered users to access the project, the related pages and linked and/or uploaded data. Link the collaborative platform with eSciDoc repository to allow long-term archiving and PIDs for content stored.

Example for shared project workflow (see details in slides (restricted):

definition of shared project and objectives
definition of required experiments
distribution of responsibilities
tracking of activities and results: set up experiments, run experiments, produce data, postprocess data, analyse data, extract scientific results
share data, combine results
produce publication-ready paper (shared authoring)

Components of the collaborative work[edit]

Collaborative work is "publication-in-progress" developed in a Wiki environment as output of the research process.
Collaborative work comprises
- textual components - mostly metadata describing textual part of a collaborative work such as: abstract, title, authors, affiliations, keywords, annotations of sources, references, and its structural information such as:subject headings, body sections etc.
- non-textual components - mostly scientific results, and representative data sets and illustrations to support the scientific results, and conclusions presented in tables and figures. Example of figures are images, plots, and diagrams etc.
- integrated external tools - interactive tools for visualization of non-textual components and manipulation of underlying data of these components, querying of remote archives etc.

Textual components[edit]

Textual components enable to:

link to references to preprints, published papers etc.(ADS, arXiv)
lookup annotated sources i.e. astronomy objects in databases such as Simbad, NED
describe the collaborative work with metadata which could be used for query such as: authors, title, abstract, keywords
describe the structure of collaborative work

Non-textual components[edit]

Non-textual components enable to:

visualy represent research data. This visual representation may have own metadata (e.g. image metadata)
show metadata for an e.g. image
invoke external data collection viewer
download data related to the component
open external tool for visualizing and working with the data
- for tabular data: e.g. TOPCAT
- for image data: e.g. Aladin
- for spectral data: e.g. SpecView, Splat, VOSpec
- PLASTIC enabled

Integrated external tools[edit]

Integrated external tools enable to link from either textual or non-textual components to existing external astronomical services or tools such as:

astronomical services - directly linked such as ADS, arXiv, NED, Simbad, VizieR, SkyServer or to enable discovery in the registries of astronomical sources
common analysis environments (IDL, ...)
services for retrieval of image data ( Simple Image Access specification SIA )
services for retrieval of spectra (Simple Spectral Access Protocol SSA)
services for retrieval records from catalogs (Simple Cone Search SCS)
simulation database SimDB (Simulation Data model and Simulation data Access Protocol SimDAP)
invoke queries on external services that support Query languages such as ADQL/TAP

Sharing of content[edit]

Enable for privileged users to upload, and /or link and describe data with metadata, comments and notes.

Standardised data: FITS, VOTable, Spectra, SQL query results
Custom data (more input needed)

Types of data[edit]

images (radio, optical, x-ray)
images (i.e.simulation)
spectra
source catalog
plot (i.e. spectrum)
diagram
flow chart
illustration
table (i.e. source catalog)
publication (textual components)

Metadata to be supported[edit]

Bibliographic metadata
- title, author, abstract, subject heading, journal metadata
Structural metadata/elements
- section/TOC, annotation, footnote, equation, caption, references
Other
- provenance (input files, make files, plotting scripts, analysis code, simulation code, ...)
- log files
- curation (more input needed)
- PIDs (ADS, IVOA)
- IVOA standards (VOTable, UCD, UTYPE, Data models, data access protocol, ...)

Shared Authoring[edit]

Author tools are provided to enable shared and standardised authoring. Authors are supported in developing publication-ready papers.

Provision of text editor (emacs? TeX IDEs?)
Import LaTeX article and conversion to html (incl. figures, tables)
Templates for publication-ready papers (metadata attachments, links, figures, captions)
allow publication-ready figures from visualisation tools

MPDL project - draft[edit]

Summary[edit]

online publications linked to/from online published data sets
networking through standardisation
collaboration enabled
focusing on scientific practice (collaboration, publication), by re-using existing data centers and resource registries, existing standards, and adding scientific "workbench-environment"
- no interruption of daily practice
- faciliate publishing of data
online environment should support
- collaborative authoring for publications in virtual organisations
- explicit integration of data sets used for/in the final publication(s) by either uploading original data or linking to external data sets
- annotation of resources with metadata and identifier according to IVOA standard
- value-added services on known data types (search, mining, visualization, analysis)
- interfaces to external archives/registries/catalogs via standard protocols
- integration of client tools (needed and known in community)
- long-term preservation of resources (publications, data, services)
- registration of resources in IVOA standard registries

Background[edit]

Results of German Astrophysical Virtual Observatory (GAVO)
- make results (data sets and services) of astronomical research easily available to community
- faciliate standardised publication of results (PIDs, Virtual Observatory standards, long-term archiving)
- focus on interoperability to enable networking (standards in use: IVOA)and automated discovery and re-use
- make use of standards-aware client tools and services (for cross-matching, visualisation, combination, data mining etc.)
Re-use of data leads to more references and scientific improvements => proof of concept Millenium Run
- community-based quality control: errors discovered by others have improved data quality
- still, as no formal revisions were made, old/original data was lost
currently, no (or limited) possibilities to add original data to publication, only representations/shortened examples:
- e.g. only image representations of multi-dimensional data
- e.g. only representative samples of large collections (images, spectra, source catalogs)
- e.g. only static data

enable the shift from large data centers/resource registries (based on IVOA, formal, machine-readable, homoegeneous) to scientific practice, i.e. collaboration and publications (informal, human-readbale, heterogeneous)

Needs[edit]

Preparatory and related work[edit]

GAVO
- stable storage and curation of data products needed
- stabe environment for deploying Virtual Observatory protocols and other value-added services
IVOA standard
AstroGrid (?)

Wider context/Re-use for others[edit]

Long-term storage of data sets used in a publication (cf. deposit mandate?)
Open access to all results of scientific research online (cf. Berlin declaration?)
Showcase for added value of implemented standards
- mandated by some funding agencies
- IVOA dataset identifier in use by ADS (main portal for astronomers)
Integration of standards, stable infrastructure and web2.0 technologies to facilitate dynamic and collaborative environments (cf. eSciDoc?)
Re-use for astronomy community within MPS
- MPI Astronomie (Heidelberg)
- MPI Astrophysik (Garching)
- MPI extraterrestrische Physik (Garching)
- MPI Gravitationsphysik (Golm)
- MPI Kernphysik (Heidelberg)
- MPI Physik (München)
- MPI Radioastronomie (Bonn)
- MPI Sonnensystemforschung (Katlenburg-Lindau)

Work description[edit]

Pilot phase[edit]

Set-up community platform for creation of shared projects, registration of users, assign privileges
- Analysis of existing community-based platforms for linking community-environment to eSciDoc repository
  - Xwiki
  - Wiki2Fedora used for MatDL/NSDL
  - other wiki software to be considered?
- Basic user management
  - Author access - authors of the project
  - Administrator access - project coordinator
  - Public access - public users
- Linking
  - to external data sets/services (URL based)
  - to eSciDoc resources (Wiki extension to support special eSciDoc tag or URL based)
Basic integration of community platform with eSciDoc pilot solution
- enable upload (or referencing) and description of data
- enable invocation of external selected visualization tool from eSciDoc pilot solution (e.g. for FITS data)
- integrate arXiv and ADS(if possible) as sources for fetching publications, pre-prints
Explore possibilities for federated search (within community platform, eSciDoc repository, 1-2 external services)

ToDo[edit]

Clarify:

which data to be supported in pilot phase
precise functional requirements for data management (Scenario level)
eSciDoc managed vs externally referenced data
formats (e.g. FITS) and how they should be supported (e.g. storage, search, visualization via external tools, etc.)
types of annotated sources and relating them to external services
available external client tools for demonstration (quick win)

Work distribution[edit]

Workpackages based on pilot approach

Wiki selection
Basic user management
Demonstrator solution
- Architecture
  - main components (wiki, eSciDoc)
  - interaction between Wiki, eSciDoc repository, eSciDoc solutions
  - identification of existing services to be involved, evtl. modification
  - checking if existing eSciDoc solutions (PubMan) can be re-used and identify necessary modifications
- Implementation

Required resources[edit]

new staff at institute(s)
new stafff at MPDL
overall costs (human resources, hardware, other)

Organisational[edit]

Institutes involved

check possibiltity of having a pilotphase with one/two institutes at start, to deliver quick and convincing results. After first showcase, other institutes can join.

Responsible for proposal
Required budget (total, annual)

Meetings[edit]

15th sept 2008[edit]

first brainstorming at MPDL/Munich

25th sept 2008[edit]

updated presentation by Gerard/Jaiwon/Wolfgang (see under SVN of MPDL (restricted)
outcome:
- First draft of MPDL project proposal until 10th of oct (Ulla, Natasa), focusing on requirements and approach
- First draft of eSciDoc HowTo for definition of high-level requirements

AWOB

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