AWOB Preparation Usage Scenarios

MPDL,GAVO

=Scenarios=

Collaborative environment
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

 * 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 representative data sets and illustrations to support the scientific results and conclusions which are presented in tables and figures. Example of figures are images, plots, and diagrams etc.
 * integrated external tools - provide links to existing external tools and services for both textual and non-textual components. This facility allows users to work in familiar environments as well as in interactive ways of visualizing and manipulating non-textual components and their underlying data presented in a collaborative work.

Textual components
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
 * Questions (JK):
 * Is a body of each section also a textual component?
 * Is an equation a textual component?
 * Figure/table caption: could it be a metadata of non-textual component?

Non-textual components
Non-textual components enable to:
 * visually represent research data and illustrations such as experiment set up. These components could be represented in tables, and figures including images, plots, and diagrams and may have own metadata (e.g. image metadata)
 * Question (JK): Could you give some specific examaples of image metadata? Depending on the context types of metadata could be quite different. For example, is it like the size, and file type of an image or more science related metadata, e.g., observation date, location, etc ?
 * Answer (NB):I think in this case we were more thinking on really image metadata such as size, resolution etc. The observation dates, location etc. would be candidate for the descriptive metadata of the item with which the image is associated.


 * show metadata for an e.g. image
 * invoke external data collection viewer
 * Question (JK): Does this mean to invoke a external tool to view the underlying data?
 * Answer (NB): Yes, there were some examples provided by you on the last meeting.


 * 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
Integrated external tools enable to link from either textual or non-textual components to existing external astronomical services or tools such as:
 * astronomical paper and data archive services - directly linked to widely used publication, and preprint archives such as ADS, and arXiv, and astronomical data archives such as NED, Simbad, VizieR and SkyServer. Also provide link to registries of astronomical resources which enable users to discover and to get connected to smaller data sets, and services.
 * common analysis environments (IDL, ...)
 * standardized data retrieval services for various types of astronomical data  compliant to IVOA standards :
 * services for retrieval of image data ( Simple Image Access Protocol SIA )
 * services for retrieval of spectra (Simple Spectral Access Protocol SSA)
 * services for retrieval records from source catalogs (Simple Cone Search SCS)
 * simulation database SimDB (Simulation Data model and Simulation data Access Protocol SimDAP)
 * invoke queries on external services that support Astronomical Data Query Language(ADQL) and Table Access Protocol(TAP). ADQL and TAP enable a general access mechanism for tabular data set not limited astronomical data.

Sharing of content
Enable privileged users to upload, and /or link and describe data with metadata, comments and notes. In astronomy some data are public which are available to everyone, and some are proprietary to a project, or to a group of collaborators. Usually data from observations become publicly available after a finite time. It is a common practice for collaborators to share their private data and their analysis in astronomy. In order to share private data, it is typical for a group of collaborators to set up a site with login/password protection, and to exchange data files mostly in FITS(Flexible Image Transport System) format with few description via ftp or xxx. For public data it is possible to access them without special permission(JK: Verify it). Due to the lack of proper metadata capture it is often difficult to utilize and to query science products and to manage them in the long term unless it is maintained by large data archives. In order to provide consistent and efficient(?) way of sharing data we provide services to upload data with proper metadata which could be used for querying, and xxxx. We support the following data formats:
 * Standardised format: FITS, VOTable,
 * Custom format: XML(?), Tabular data in comma/tab separated(more input needed)
 * Questions (JK)
 * Could textual and non-textual components of a collaborative work be a sharing content? Somehow I assume that content in this section is limited to astronomical data.
 * Do we need to describe public/private data, as well as raw data/science product somewhere?
 * I put a few points that might be appeared/clarified on this section. Please ignore messiness.

Types of Astronomical Data

 * images (from observations, simulations, and etc )
 * spectra
 * source catalog
 * More inputs(Any data which could be in FITS binary table)
 * time series
 * good time intervals
 * light curves
 * source extraction(?)

Auxiliary data types

 * diagram
 * flow chart
 * illustration
 * publication (textual components)

Metadata to be supported

 * Bibliographic metadata
 * title, author, abstract, subject heading, journal metadata
 * Structural metadata/elements
 * section/TOC, annotation, footnote, equation, caption, references
 * Astronomical metadata
 * FITS keywords, values, and comments
 * taItalic textbular data column name
 * Other
 * provenance (input files, make files, plotting scripts, analysis code, simulation code, ...)
 * Comment (JK): analysis code, and simulation code may be moved to Astronomical metadata


 * log files
 * curation (more input needed)
 * PIDs (ADS, IVOA)
 * IVOA standards (VOTable, UCD, UTYPE, Data models, data access protocol, ...)
 * Comment(JK): I don't think IVOA standards belong here.

Shared Authoring
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
 *  Questions (JK):
 * How does one distinguish 'publication-ready' from 'publication-in-progress'?
 * Does publication-ready mean to review the result of 'publication-in-progress' phase?

=Related tools/projects=
 * report on Virtual Research Communitues
 * ARCHER project
 * eSciDoc.Faces allows publishing of images and respective subsets (albums). Provides technical metadata extraction.
 * My experiment Find, use, share objects and workflows, community building. Provides REST interfaces, includes Taverna as Workflow Workbench
 * HyperImage for describing, relating details within images
 * XWiki Java-based wiki
 * SweetWiki another Java-based wiki
 * Trident Microsoft product, a "scientific workflow workbench"
 * Demonstrator Driver for enhanced publications (embedded queries within publication, usage of OAI-ORE)
 * TOPCAT tool for operations on catalogs and tables
 * eBank UK project
 * Jisc StORE project, seems project wiki is not available