|ID/Description||Part of||Reporter||Due date||Completed||Document/URL||Details|
|M5.10 - API design plan||D5.1 - Prototype workflows and API||Neil Caithness||Fri, 31/12/2010||Completed|
|M1.10 - Confirmation of year 1 meeting dates||Dave Roberts||Fri, 31/12/2010||Completed|
|M1.11 - Circulation of next meeting agenda||Dave Roberts||Fri, 31/12/2010||Completed|
|M1.12 - Organise kick-off meeting||Dave Roberts||Fri, 31/12/2010||Completed|
|M1.13 - Minutes of management committee meetings||Dave Roberts||Mon, 28/02/2011||Completed|
|M1.14 - Minutes of strategic board meetings||Dave Roberts||Mon, 28/02/2011||Completed|
|M5.11 - Review existing key construction software and workflow interaction with both Scratchpads and the CDM||D5.2 - Functional tools||Régine Vignes-Lebbe||Mon, 28/02/2011||Completed||
Identification of specimens and observations is a crucial task . Today
In this document we make a short review of existing key construction software for these three
|M5.12 - Review user requirements for the visualisation tool for Scratchpads||D5.2 - Functional tools||Javier de la Torre||Mon, 28/02/2011||Completed|
|M6.10 - Use cases of existing standards of XML mark up tagging and semantic enhancement collected and review||D6.1 - XML mark up tool & service||Lyubomir Penev||Mon, 28/02/2011||Completed|
|M5.13 - API baseline documentation||D5.1 - Prototype workflows and API||Milo Thurston||Thu, 31/03/2011||Completed||
The system is designed to accept input directly from a Scratchpad server by means of JSON requests. Thus, only one account (the Scratchpad server's) will be required to send data, and the Scratchpad server will deal with presenting these data to the user. However, a web interface with separate user accounts has also been added so that jobs may be submitted without the use of a Scratchpad, if necessary. JSON authentication requires a unique identifying string which is not enabled by default for users; this must be done manually by the sysadmin for any user who plans to access this interface.
Information on the use of the JSON interface can be obtained by users with an "admin" account by visiting the /docs or /info URLs on the running application. The former gives brief details on the use of the interface and the latter lists all "routes" available, i.e. actions that can be called on the application. The routes information is generated automatically and the docs information is updated manually as the application is developed. The output is attached as a text file.
The application is currently under version control and is running at https://vibrant.oerc.ox.ac.uk.
|M5.14 - Review of target applications (phylogenetics)||D5.2 - Functional tools||Neil Caithness||Thu, 31/03/2011||Completed||
A few comments:
We have been investigating a one-click process from data retrieval (molecular) to alignment and phylogenetic analysis along the lines of 2 above. For data retrieval we have experimented with Genbank, for allignment with Clustalw and Mussle, and for phylogenies, Phylip. Automating a seemless process is not straightforward and without risks but we believe it is achievable withing the OBOE framework.
|M1.15 - Circulation of next meeting agenda||Dave Roberts||Sat, 30/04/2011||Completed|
|M5.15 - API version control||D5.1 - Prototype workflows and API||Neil Caithness||Sat, 30/04/2011||Completed||
The API is fully documented and has been under version control since April.
The documentation was last updated on Tue Jun 28 12:18:20 BST 2011
|M2.10 - Test version of distributed Scratchpad server||D2.1 - Distributing servers||Simon Rycroft||Tue, 31/05/2011||Completed||
Deliver a test version of the mechanism to distribute the Scratchpad servers across multiple institutions
|M2.11 - Report on Scratchpad usage statistics options||D2.2 - Scratchpad Registry||Simon Rycroft||Tue, 31/05/2011||Completed|
|M4.10 - Define methods to use the Scratchpad service layer deliverable within the CDM store||D4.1 - Scratchpad common access point||Olaf Bánki||Tue, 31/05/2011||Completed||
Partly for PESI application. Responsible partners: UvA & BGBM
|M4.11 - Prototype of collaborative community interface||D4.1 - Scratchpad common access point||Gregor Hagedorn||Tue, 31/05/2011||Completed|
|M8.10 - Prototype ecological and conservation applications||D8.1 - Scratchpad modules engaging citizen scientists||Christos Arvanitidis||Tue, 31/05/2011||Completed||
Modified from "Prototype scratchpads modules with ecological and conservation applications" to better align with the evolving WP5 platform for analytical services.
Also available from the git repository (https://git.scratchpads.eu/viewgit?p=indices.git;a=summary)
|M7.10 - Agreement of standard format for community contributed bibliographies in conjunction with WP4||D7.1 - Community contributed bibliography||David Morse||Fri, 17/06/2011||Completed||
The report is complete and the platform for D7.1 has been agreed. WP7 will use the Drupal biblio module as the basis for implementation, hosted in a Scratchpad. Thus the supported formats will be those provided by the biblio module, such as BibTex and RIS
|M7.11 - Review of options for interactive mark up tools within the Scratchpad infrastructure||D7.2 - Mark-up modules||David Morse||Fri, 17/06/2011||Completed||
The report is complete although since this report is being prepared in a Wiki, it is a ‘living document’ so it will be updated as and when necessary.
|M1.16 - Minutes of management committee meetings||Dave Roberts||Thu, 30/06/2011||Completed|
|M1.17 - Minutes of strategic board meetings||Dave Roberts||Thu, 30/06/2011||Completed|
|M5.16 - Review of target platforms and requirements||D5.3 - Sustainable software services||Neil Caithness||Thu, 30/06/2011||Completed||
The platform requirements review has been superseded by full implementation for services on both Unix and Windows systems.
We have in principle agreements and a free allocation of startup CPU hours to run services on the OSC clusters and on NGS resources.
A simple service API is now in place that will allow any authenticated Windows or Unix machine, located anywhere on the internet, to run OBOE services.
|M4.12 - Liaison and networking with ontology experts and existing ontology providers||D4.2 - Ontology tools||David Remsen||Sun, 31/07/2011||Completed||
Producing a dynamic catalogue of resources.
|M6.11 - Prototype and beta-version of XML submission from Scratchpads to publishers||D6.1 - XML mark up tool & service||Dave Roberts||Sun, 31/07/2011||Completed||
A short decsription of the prototype of the publishing module, including screenshots of the steps.
|M7.12 - A suite of test cases that will be used to test the de-duplication software||D7.1 - Community contributed bibliography||David Morse||Sun, 31/07/2011||Completed||
The milestone report documents progress towards the suite of test cases and presents the case for using existing large databases and the duplicates that they contain for testing purposes.
|M7.13 - Review of options to use typographical information and other contextual clues||D7.2 - Mark-up modules||David Morse||Sun, 31/07/2011||Completed||
This is to identify and tag document content by type. The Milestone report consists of a short overview document and a much larger report on the existing GoldenGATE modules.
As noted in the Milestone overview document, we think there is scope to publish a narrative review of the problem of using typographical information and other contextual cues but this review has not been written yet.
|M1.19 - Preparation of first JPA templates||Dave Roberts||Wed, 31/08/2011||Completed||
The project reporting templates were received from Brussels on 13th December. This document is dated 2010, but we had no confirmation that we were still using the same structure.
In fact we have enough information from the project milestones and ZooKeys special issue to complete them, at least to first draft, so templates are unnecessary. Cover templates are available from the resources pages of the web site.
|M4.13 - Release an API on the catalogue of resources||D4.1 - Scratchpad common access point||Gregor Hagedorn||Wed, 31/08/2011||Completed||
For accessing existing ontology resources within Scratchpad sites
|M1.18 - Circulation of next meeting agenda||Dave Roberts||Fri, 30/09/2011||Completed|
|M3.10 - Delivery of a promotional strategy for ViBRANT services||D3.2 - Service delivery and evaluation||Thierry Backeljau||Fri, 30/09/2011||Completed||
This document focuses mainly on setting the grounds for a ViBRANT promotional strategy and plan, mapping foreseen outreach activities for the duration of the project.
|M6.12 - Workshop on mark up tagging tools and implementations||D6.1 - XML mark up tool & service||Lyubomir Penev||Mon, 31/10/2011||Completed||
The milestone report consists of two meeings on XML mark up schemas and tagging tools held in Paris (during the kick-off) minutes and presentations
Note: these workshops were originally conceived to take place at TDWG meetings, but the most significant meetings were those reported here.
|M7.14 - Collaboration with WP6 on mark-up tagging tools and implementation||D6.1 - XML mark up tool & service||David Morse||Mon, 31/10/2011||Completed||
The report contains a brief summary of some of the ways in which members of WP6 and WP7 have collaborated on XML mark-up and tagging tools.
|M1.20 - Minutes of management committee meetings||Dave Roberts||Fri, 18/11/2011||Completed||
Delivery date was modified to match the actual meeting date, which was postponed due to a conflict with the TDWG conference.
|M8.11 - Review of relevant field recording tools and applications||D8.1 - Scratchpad modules engaging citizen scientists||Alexander Kroupa||Fri, 25/11/2011||Completed||
These support biodiversity inventory and monitoring programs
|D3.1 - Training strategy||D1.1 - Overall Management||Thierry Backeljau||Tue, 29/11/2011||Completed||
Full strategy for training and delivery, tested on an initial training course and with training course announcements and workshops for the next year.
|M3.12 - Assessment of user support services, with the refinement of subsequent milestones||D3.1 - Training strategy||Thierry Backeljau||Tue, 29/11/2011||Completed||
Scratchpads user support systems are analysed and discussed. Results of a maintainer survey will feed into the development and project management of Scratchpads.
|D2.1 - Distributing servers||D1.1 - Overall Management||Simon Rycroft||Wed, 30/11/2011||Completed||
The Scratchpad Mirror server is: http://e090.bgbm.fu-berlin.de/
Distribute the Scratchpads across multiple servers and institutions
|D4.1 - Scratchpad common access point||D1.1 - Overall Management||Yde de Jong||Wed, 30/11/2011||Completed||
Develop an initial set of API services to link the Scratchpad communities to the resources of the CDM, to facilitate data exchange. Specifically these will implement a persistent identifier framework for shared objects between Scratchpads and the CDM to facilitate the identification of object changes, deletions and additions in linked databases.
|D5.1 - Prototype workflows and API||D1.1 - Overall Management||Neil Caithness||Wed, 30/11/2011||Completed||
The sustainable integration of external tools and services into the Scratchpad environment requires a well designed and documented API. In this task we will work closely with WP4, specifically Task 4.4 (Standard data interfaces and APIs) to ensure that the tools API is consistent with development of a data API. The tools API specification and documentation will to be maintained under strict change control.
|D6.1 - XML mark up tool & service||D1.1 - Overall Management||Lyubomir Penev||Wed, 30/11/2011||Completed||
XML mark up tool to create ready-to-submit taxonomic manuscripts from Scratchpads to ZooKeys and PhytoKeys. Create a service to preview service for author-proofing prior to formal submission.
Description of the workflow with implementation shown with the exemplar paper of Faulwetter et al. (2011)
|D7.1 - Community contributed bibliography||D1.1 - Overall Management||David Morse||Wed, 30/11/2011||Completed||
Prototype Service: http://plazi2.cs.umb.edu:8080/RefBank/search
A functional community-contributed bibliography with unique identifiers at publication unit level(s) and links to publicly available digital copies where possible.
The report contains a description of the community constructed bibliography, covering:
The prototype is hosted at http://plazi2.cs.umb.edu:8080/RefBank/search
For reasons why this is still a prototype, please see the deliverable report.
|D8.1 - Scratchpad modules engaging citizen scientists||D1.1 - Overall Management||Christos Arvanitidis||Wed, 30/11/2011||Completed||
COMBER site (beta version); *.pdf document
Scratchpad modules with APIs for engaging citizen scientists to facilitate i) observation data entry and correction; ii) a demonstration project with marine naturalists; and iii) field recording tools (mobile App. Development).
|M1.21 - Confirmation of year 2 and 3 meeting dates||Dave Roberts||Wed, 30/11/2011||Completed||
Schedule agreed at Management Committee #3
|M2.12 - Ongoing module development supporting prioritised features requested by users through WP3||D2.1 - Distributing servers||Simon Rycroft||Wed, 30/11/2011||Completed|
|M2.13 - Define further milestones in the light of usage and feedback||D1.1 - Overall Management||Simon Rycroft||Wed, 30/11/2011||Completed|
|M4.14 - Define further milestones in the light of usage and feedback||D1.1 - Overall Management||Yde de Jong||Wed, 30/11/2011||Completed|
|M5.18 - Review user requirements for enhanced user interface||D5.1 - Prototype workflows and API||Neil Caithness||Wed, 30/11/2011||Completed||
At the start of the project it seemed likely that there would be an external user interface for computing services. The final design and implementation of OBOE and the OBOE API has made this requirement obsolete. No external user interface is required and all user interaction is done via simple web-forms implemented in Scratchpads using information retrieved from the OBOE API queries for specific service types.
|M5.19 - Deliver prototype key-generating service through Scratchpads||D5.2 - Functional tools||Régine Vignes-Lebbe||Wed, 30/11/2011||Completed|
|M6.13 - Define further milestones in the light of usage and feedback||D1.1 - Overall Management||Lyubomir Penev||Wed, 30/11/2011||Completed||
List of two additional milestones planned for the second period if ViBRANT.
|M8.12 - Identify rules for an intelligent algorithm to identify suspicious data records in GBIF data||D8.3 - A start-up portal for discovery of GBIF mediated data||David Remsen||Wed, 30/11/2011||Completed||
Slide show presented in TDWG Conference (geospatial before and after on slides 8/9, taxonomic before and after are on slides 10 and 12)
|M8.13 - Define further milestones in the light of usage and feedback||D1.1 - Overall Management||Christos Arvanitidis||Wed, 30/11/2011||Completed|
|M8.14 - Prototype demonstration project with non-professional marine naturalists||D3.1 - Training strategy||Christos Arvanitidis||Wed, 30/11/2011||Completed||
Paper describing the COMBER project
|M1.22 - Circulation of next meeting agenda||Dave Roberts||Sat, 31/12/2011||Completed|
|M1.23 - First year financial reports||D1.1 - Overall Management||Dave Roberts||Sat, 31/12/2011||Completed|
|M4.15 - Ontology Tools: migrate GBIF Vocabularies Service||D4.2 - Ontology tools||Dag Endresen||Sat, 31/12/2011||Completed||
Description:Migrate the GBIF Vocabularies Service from the Scratchpads server hosted by the Natural History Museum in London to new servers hosted by the GBIF Secretariat in Copenhagen for improved performance.
Deadline: 31 December 2011.
|M4.16 - Ontology Tools: scoping document on a KOS architecture||D4.2 - Ontology tools||Yde de Jong||Sat, 31/12/2011||Completed||
GBIF has prepared a draft charter proposing to form a new TDWG task group on a Vocabulary Management (VMTG). The VMTG proposal focuses on tools for managing a new glossary of basic terms. The present tools to create Darwin Core extensions and vocabularies for the GBIF infrastructure does not include such a basic overview list of the terms that are defined and reused by the extensions and vocabularies.
Description: Prepare scoping document on a KOS architecture for the GBIF network including the requirements for a new ontology
Deadline: First draft scoping document finalized by 31 December 2011
|M5.20 - Metadata repository design plan||D5.2 - Functional tools||Neil Caithness||Sat, 31/12/2011||Completed||
In order to hold the specifications for tasks to be submitted to external computing services we will design a metadata repository to be integrated with Scratchpad instances. This repository will hold job specifications, and the history of results. It will be exposed to the Scratchpad user via the enhanced user interface developed in Task 5.8.
|M6.14 - Review of existing standards of semantic enhancements to taxonomic papers||D6.2 - Review, refine & evaluate services||Lyubomir Penev||Sat, 31/12/2011||Completed|
|M3.11 - Potential Mechanisms to increase user uptake||D3.3 - Community delivery and evaluation||Peter van den B...||Fri, 13/01/2012||Completed||
[Criteria for evaluation are outlined in the DoW.]
This milestone discusses
The submission date of the
|M1.24 - First year annual progress report||Dave Roberts||Tue, 31/01/2012||Completed|
|M6.19 - XML export format of metadata on identification keys to Key Central (ALA)||D6.3 - Data publication workflow||Lyubomir Penev||Tue, 31/01/2012||Completed||
This milestone intends to set up an automated workflow for exporting metadata on identification keys published in scholarly journals to KeyCentral. KeyCentral is an index of identofication keys launched by Identifylife.org and supported by the Atlas of Living Australia. The milestone will list the XML metadata format which any publisher might use to export the identification keys to that centralized index.
|M4.17 - Extensions for DwC-A export functionality||D4.1 - Scratchpad common access point||Yde de Jong||Tue, 28/02/2012||Completed|
|M1.25 - Minutes of management committee meetings||Dave Roberts||Wed, 29/02/2012||Completed|
|M1.26 - Minutes of strategic board meetings||Dave Roberts||Wed, 29/02/2012||Completed||
No strategic board meeting has been called.
|M5.21 - Implement visualisation tool for Scratchpads||D5.2 - Functional tools||Javier de la Torre||Wed, 29/02/2012||Completed||
Version 1 of the tool is available at:
|M5.22 - Review algorithms for biodiversity indices||D5.2 - Functional tools||Javier de la Torre||Wed, 29/02/2012||Completed|
|M7.15 - Define further milestones in the light of usage and feedback||D1.1 - Overall Management||Dauvit King||Wed, 29/02/2012||Completed||
Additional milestones defined to monitor and break down work programme for year 2. Milestones added to the list of milestones and deliverables on the ViBRANT website.
|M4.18 - Human Interface for CDM-ViBRANT Index||D4.1 - Scratchpad common access point||Yde de Jong||Wed, 28/03/2012||Completed||
Description: User Interface for CDM-ViBRANT Index functional. Implementation of a simple query interface that allows humans to query the service for names only (across all classifications stored in the CDM).
|M1.27 - Organise mid-project meeting||Dave Roberts||Sat, 31/03/2012||Completed||
Deprecated. The Management Committee decided to organise a number of focused meetings to which external collaborators could be invited. The funds that would have been devoted to the mid-project meeting will instead be used for partners to attend these smaller, topic-focused meetings.
|M5.23 - Implementation of platforms specific middleware||D5.3 - Sustainable software services||Neil Caithness||Sat, 31/03/2012||Completed|
|M5.24 - Implement application specific wrappers (phylogenetics) that can be used by Scratchpads||D5.3 - Sustainable software services||Neil Caithness||Sat, 31/03/2012||Completed|
|M5.25 - Implement custom wrapper for the identification service that can be used by Scratchpads||D5.2 - Functional tools||Neil Caithness||Sat, 31/03/2012||Completed|
|M6.20 – Beta version of XML queries to IPNI and ZooBank||D6.3 - Data publication workflow||Lyubomir Penev||Sat, 31/03/2012||Completed||
The aim of this milestone will be to identify and test the approproiate format of XML queries and back reports with two important registries of taxon names - the International Plant Name Index (IPNI) mainteined at Kew Gardens, UK, and ZooBank currently maintained at the Bishop Museum, Honolulu, USA. The milestone will list the beta versions of the XML queries which can be used by publishers to set up automated registration workflows with IPNI and ZooBank.
|M7.21 Add metadata to cover origin of bibliographies||D7.3 - Literature search||Dauvit King||Fri, 13/04/2012||Completed||
Metadata and processing code added to RefBank to cover origin of bibliographies.
These ideas of origin could also be extended to attribute contributions made by people editing a reference.
This milestone was defined in M7.15.
|M1.28 - Circulation of next meeting agenda||Dave Roberts||Mon, 30/04/2012||Completed|
|M4.20 - Ontology Tools: new prototype (GBIF) Glossary of Terms registry||D4.2 - Ontology tools||Dag Endresen||Mon, 30/04/2012||Completed||
Description: Develop a new prototype (GBIF) Glossary of Terms registry for terms used by the ViBRANT and GBIF infrastructure.
Deadline: April 2012
|M7.22 Import bibliographies from Pensoft to RefBank||D7.3 - Literature search||Dauvit King||Fri, 04/05/2012||Completed||
Develop the infrastructure to import bibliographic information automatically from Pensoft to RefBank. Typically, this will be the metadata about each publication and the bibliography from the end of the paper. Note that this milestone relies on there being a working attribution (origin) mechanism - see Milestone M7.21.
This milestone was defined in M7.15.
|M4.19 - Canvassing glossary-oriented potential contributors||D4.2 - Ontology tools||Yde de Jong||Wed, 16/05/2012||Completed||
Description: We had several contacts, but so far they did not work out. We have concretely Milestone M4.22 as a fall-back, but we would like to introduce a Milestone to verify that we have no better opportunity to provide a more international, english language, convincing demo. This involves further follow-ups of earlier discussions within ViBRANT (GBIF, NHM) as well as outside. MEMO to self: actually go public on Taxacom?
Comment Yde: BGBM promised also to provide some user-cases using CDM content in the Scratchpads, but also using CDM content in the MediaWiki's. These could be included in this milestone. In addition, the idea to use the http://bionomenclature-glossary.gbif.org/ as a demo, seeing how it compares in mediawiki, could be surveyed here. So apart from looking for potential media-wiki contributors, this milestone should also anticipate on increasing the (content based) interaction between the different platforms.
Original Deadline: 31 March 2012
|D2.2 - Scratchpad Registry||D1.1 - Overall Management||Simon Rycroft||Thu, 31/05/2012||Completed||
Develop registry of Scratchpad sites and Scratchpad API's that includes detailed usage statistics data
|M2.14 - Report on the data search portal providing a single point of entry to all Scratchpad data completed||D2.1 - Distributing servers||Walter Berendsohn||Thu, 31/05/2012||Completed|
|M5.17 - Define further milestones in the light of usage and feedback||D1.1 - Overall Management||Neil Caithness||Thu, 31/05/2012||Completed|
|M7.23 Extend RefBank import routines to support other widely used bibliographic formats, eg BibTex, RIS, etc||D7.3 - Literature search||Dauvit King||Fri, 01/06/2012||Completed||
As the milestone states, RefBank needs extending so that import from other widely used bibliographic formats such as BibTex and RIS are supported. This will facilitate populating the database by bulk upload of personal bibliographies. Note that this milestone relies on there being a working attribution (origin) mechanism - see Milestone M7.21 - if people who upload their bibliographies are to be credited. Bulk upload will be implemented by Milestone M7.24.
This milestone was defined in M7.15.
Milestone original delivery date was Friday 29 June 2012.
|M7.24 Upload service for complete bibliographies||D7.3 - Literature search||Dauvit King||Fri, 01/06/2012||Completed||
In order to allow individuals to upload bibliographies that they have compiled, a bulk upload service is required. This milestone will address that requirement. M7.24 requires the functionality that will be developed in M7.21, M7.22 and M7.23.
This milestone was defined in M7.15.
Milestone original delivery date was Friday 29 June 2012.
|M1.29 - Minutes of management committee meetings||Dave Roberts||Sat, 30/06/2012||Completed|
|M1.30 - Minutes of strategic board meetings||Dave Roberts||Sat, 30/06/2012||Completed|
|M5.26 - Review of target applications (bioclimatic modelling)||D5.2 - Functional tools||Neil Caithness||Sat, 30/06/2012||Completed|
|M4.21 - Ontology Tools: new prototype Biodiversity BioPortal||D4.2 - Ontology tools||Dag Endresen||Tue, 14/08/2012||Completed||
Description: Present a new prototype Biodiversity BioPortal based on the NCBO BioPortal. This platform will be used for hosting vocabularies and ontologies for new data types (in addition to the DwC Occurrence and DwC Taxon).
Deadline: June 2012
|M1.31 - Circulation of next meeting agenda||Dave Roberts||Fri, 31/08/2012||Completed|
|M1.32 - Preparation of second JPA templates||D1.1 - Overall Management||Dave Roberts||Fri, 31/08/2012||Completed||
Depricated JPA templates are not being used in the project. Project planning is detailed on this web site and can be followed through the milestones and deliverables, or in narrative form from the home page.
|M4.39 - Term browser||D4.2 - Ontology tools||Dag Endresen||Sat, 01/09/2012||Completed||
Develop a term browser for improved discovery of vocabulary terms used for documentation of biodiversity information resources.
The prototype application (http://kos.gbif.org/termbrowser/) allows a user to browse for terms defined in widely used vocabularies such as Darwin Core, Dublin Core, FOAF, etc., including, where available, translations. The idea is to allow someone to quickly see if a term already exists so they can re-use it rather than minting it afresh. This application is purely for searching and browsing and does not replace the need for tools such as ISOcat and Semantic MediaWiki as collaborative platforms for actually creating vocabularies (and translations).
The term browser application is based on Solr, the technology also used for the GBIF occurrence/names index. It allows highly flexible, faceted searching. The facets provided are vocabulary, type (class or property) and language.
|M7.16 - Mark-up modules delivering outline mark-up||D7.2 - Mark-up modules||Dauvit King||Fri, 28/09/2012||Completed||
E.g. for article boundaries, treatment boundaries, headings and authors
Milestone original delivery date was Thursday 31 May 2012.
Deferred to Friday 29 June 2012 in line with changing emphasis within WP7 to favour progress on bibliographic reference handling at the expense of mark up processing. See milestones M7.23 and M7.24.
Deferred again - see Rescheduling below.
|M4.23 - Scratchpad to DwC-A Mapping Module||D4.1 - Scratchpad common access point||Yde de Jong||Sun, 30/09/2012||Completed||
Description: User interface for flexible mapping of Scratchpad 2 to DwC-A
|M4.24 - Full text search CDM-ViBRANT Index||D4.1 - Scratchpad common access point||Yde de Jong||Sun, 30/09/2012||Completed||
Description: Full text search functional. Specification and Implementation of a simple query interface that allows humans to perform full text searches.
|M4.25 - Pilot implementation of webservice at BGBM||D4.1 - Scratchpad common access point||Yde de Jong||Sun, 30/09/2012||Completed||
Description: Pilot deployment of the ViBRANT Single Access Key Service in the Platform (Hackaton)
Partners: BGBM & UPMC
|M4.27 - Audubon Core standard on Mediawiki||D4.2 - Ontology tools||Yde de Jong||Sun, 30/09/2012||Completed||
Description: In the first year, the taxpub standard was documented on the vibrant biowikifarm and forms for text and semantic linking developed. The Audubon Core standard for media data, jointly developed by GBIF and TDWG (and already integrated into the GBIF IPT) is presented on the ViBRANT biowikifarm as its primary location. Audubon Core is presently under public review which is part of the TDWG standardization process. To further the use of the ViBRANT/GBIF KOS platform, the Audubon Core terms are already atomized, i.e. each term on its own page, and with full semantic linking between them (see http://terms.gbif.org/wiki/Audubon_Core ).
We will use this as a demo for "developed", static standards.
Deadline: 9 September 2012
|M5.27 - Metadata repository implementation||D5.3 - Sustainable software services||Neil Caithness||Sun, 30/09/2012||Completed||
In order to hold the specifications for tasks to be submitted to external computing services we will design a metadata repository to be integrated with Scratchpad instances. This repository will hold job specifications, and the history of results. It will be exposed to the Scratchpad user via the enhanced user interface developed in Task 5.8.
|M5.33 – Generic computational framework for geo-spatial analysis via OBOE.||D5.2 - Functional tools||Neil Caithness||Sun, 30/09/2012||Completed||
A suite of computational services for geo-spatial analysis will be developed for Scratchpads via the OBOE (https://oboe.oerc.ox.ac.uk/) infrastructure.
The current focus of many (or even most) Scratchpads is on taxonomic groups – this was the original intended use. A new set of geo-spatial tools will facilitate an alternative focus on geographic regions – e.g. protected areas, game reserves and national parks. Equally, non-protected areas, agricultural lands, urban/rural interfaces, etc., may all be spatially demarcated areas of interest for the Scratchpad community of users.
These tools will provide a rich set of maps and other analytical graphics, as well as download links for the associated regional data subsets in standard formats for further analysis by the user.
A generic software framework and template for drop-and-compute services has been developed. This framework will provide for rapid and efficient development of the planned ecological informatics services detailed in milestones M5.34 - M5.36
|M8.15 - Report on existing processing services and analytical services||D5.2 - Functional tools||Christos Arvanitidis||Sun, 30/09/2012||Completed||
This field of research development is vast and fast evolving over the last couple of decades. The scientific community has made such a progress that at the moment it is not possible to know even the exact number of the facilities existing for the process and analysis of information and data relevant with the disciplines of taxonomy, biogeography and ecology. Therefore, this analysis must be restricted to a set of services available on the internet which are manageable in terms of numbers, operational features and use. For this reason only those offered by the mostly used sites (e.g. WoRMS, FishBase, GBIF, OBIS, uBIO, etc.) have been included in this report.
|M8.16 - Prototype analytical tools and reporting tools implemented on the visualization tool||D8.2 - Analytical and reporting tools||Javier de la Torre||Sun, 30/09/2012||Completed||
Originally scheduled for 31st May 2012. Delayed with agreement by VS until end of September when Vizzuality release Cartodb 2.0.
|M8.17 - APIs to integrate various data sources in support of analytical and reporting tools||D5.2 - Functional tools||Christos Arvanitidis||Sun, 30/09/2012||Completed||
The issue of the implementation of these routines to the ViBRANT Infrastructure has been solved in collaboration with WP5. The routines will be made available by OBOE. This was decided in order to avoid to have multiple ways and services through which the calculation routines would be available. The templates with the types of data needed and the kinds of output calculations have been delivered to WP5 leader along with the respective routines (scripts in C++).
|M8.19 - Data flow from GBIF annotation module to Biodiversity Data Journal||D6.3 - Data publication workflow||Lyubomir Penev||Sun, 30/09/2012||Completed||
Data flow from GBIF annotation module to Biodiversity Data Journal
|M1.33 - Minutes of management committee meetings||D1.1 - Overall Management||Dave Roberts||Wed, 31/10/2012||Completed|
|M7.25 Enhance reference parser to parse references in bulk uploads||D7.3 - Literature search||Dauvit King||Wed, 31/10/2012||Completed||
Opening RefBank to allow people to upload references requires that the reference parser is enhanced so that it can cope with the variety of formats that will be presented. This is not simply to cope with well-structured references that adhere to reference format standards, but also common mistakes and errors in the formats. M7.25 builds on the functionality that will be developed in M7.21, M7.22, M7.23 and M7.24.
Actually completed earlier, but only got around to writing the report today, Tuesday 30 October 2012. Dauvit
|M7.17 - Review of pilot mark up processes within the Scratchpad infrastructure||D7.2 - Mark-up modules||Dauvit King||Fri, 23/11/2012||Completed||
Originally planned for 31 July 2012. However, following confirmation at ManComm7 to pull forward bibliographic work in preference to data mining work this milestone was deferred. Delivery date further affected by re-plan to include more enhancements to RefBank during year two than originally envisaged.
Eventually re-scheduled in line with revised date for M7.16 (http://vbrant.eu/content/m716-mark-modules-delivering-outline-mark). M7.16 was completed 28 September 2012.
After allowing for TDWG and similar interruptions, this milestone would have to be deferred to a realistic date in mid-November. Finally moved to 23 November 2012 at the end of three one-day workshops that week in which mark-up processes, and their integration with both Scratchpads and OBOE, feature heavily.
Satisfactorily reviewed in our workshop at Oxford on Wednesday 21 November 2012 (http://vbrant.eu/content/three-days-workshops) hence marked as complete. The accompanying report will be written next week after the rest of this week's workshops are out of the way.
Update: report completed Tuesday 27 November 2012.
|M3.14 - Assessment of user support services and promotional activities||D3.2 - Service delivery and evaluation||Thierry Backeljau||Wed, 28/11/2012||Completed||
The different support systems of the Scratchpad platform are evaluated by means of an online survey and feedback forms. Data are provided to evaluate the success of the outreach activities. The report also includes the refinement of subsequent milestones.
|D7.2 - Mark-up modules||D1.1 - Overall Management||Dauvit King||Thu, 29/11/2012||Completed||
This deliverable involved extending and integrating the GoldenGATE interactive mark-up tool (http://plazi.org/?q=GoldenGATE) within the Scratchpad infrastructure. GoldenGATE is our tool of choice because it has the mechanisms for handling the stylised structures common in taxonomic literature. Should integration of the complete tool prove difficult, GoldenGATE’s modular structure will permit it to be decomposed so that individual modules can be integrated into the Scratchpad infrastructure or deployed as web services.
Having established that GoldenGATE could not integrate easily with the new infrastructure, the primary achievement of Year Two is the reworking of GoldenGATE functionality into discrete web services. These are available as standalone RESTful calls and through WP5’s OBOE service (https://oboe.oerc.ox.ac.uk/). Through the application of the individual GoldenGATE web services we will be able to achieve all elements of this deliverable.
|D3.2 - Service delivery and evaluation||D1.1 - Overall Management||Peter van den B...||Fri, 30/11/2012||Completed||
|D5.2 - Functional tools||D1.1 - Overall Management||Neil Caithness||Fri, 30/11/2012||Completed||
Release of functional tools as products accessible through the API.
|D6.2 - Review, refine & evaluate services||D6.2 - Review, refine & evaluate services||Lyubomir Penev||Fri, 30/11/2012||Completed||
Review & refine existing services in the light of user feedback and usage statistics. Evaluate and refine XML schemas for submitting submission.
Original delivery date: 31 May 2012
Deliverable describes the feedback from online surveys aimed at finding user’s attitude towards the Pensoft’s Online Publishing platform and the overall structure, interface and functionality of the Pensoft Writing Tool. Pensoft's approach has been widely welcomed within the taxonomic community as is evident by the largely positive comments received to the surveys and the very rapid response to the call for editors for the Biodiversity Data Journal. Respondents have reported some technical problems and suggested how to improve the interface and functionalities of the PWT. TaxPub XML schema that has hitherto been used by Pensoft were significantly expanded to reflect the specifics of each of the different publication templates in the PWT and Biodiversity Data Journal.
Deliverable delayed by the decision to expand functionality of the Pensoft Writing Tool (PWT) to support the new Biodiversity Data Journal. This will allow completion of the deliverable as anticipated, but with a significantly expanded journal structure and better sustainability model.
|D8.2 - Analytical and reporting tools||D1.1 - Overall Management||Javier de la Torre||Fri, 30/11/2012||Completed||
The delivery of Analytical and reporting tools include two main software packages:
1) GeoCAT: This tool is designed to produce rapid species level conservation assessments based on IUCN Red List Categories and Criteria (IUCN 2001). Through an easy to use interface with a familiar Google Map underlay you can upload primary occurrence data for a species and at the click of a button calculate values relating to the geographic range of a species.
2) CartoDB: An Open Source project to enable analysis and visualizations of geospatial data. The tool has been created in a very generic way to enable many different analysis and reporting use cases. CartoDB has been upgraded to 2.0 to focus on usability and performance.
In this report we include a description of the different components being developed by Vizzuality. During the development several workshops had been organized to engage with future users and help them adopt the new technology.
|M2.16 - Localised unit testing mechanism||D2.4 - Unit testing||Simon Rycroft||Fri, 30/11/2012||Completed||
Testing of a localised unit testing mechanism for Scratchpad code in preparation for completion of a distributed system
The deadline for this milestone was pushed back so that we could take greater advantage of the work we have carried out on upgrading Scratchpads 1.0 sites to Scratchpads 2.0. It also made sense to push this back, as the Deliverable it is associated with is not being delivered until month 36.
|M2.17 - Ongoing module development supporting prioritised features requested by users through WP3||D5.3 - Sustainable software services||Simon Rycroft||Fri, 30/11/2012||Completed|
|M3.13 - Recommendations to modify products||D3.2 - Service delivery and evaluation||Peter van den B...||Fri, 30/11/2012||Completed||
This is to maximise user uptake in the light of experience of the previous adjustments.
|M4.28 - Statistical output provided for CDM-ViBRANT Index query Interface||D4.1 - Scratchpad common access point||Yde de Jong||Fri, 30/11/2012||Completed||
Description: Specification and Implementation of statistical output in the CDM-ViBRANT Index query interface (data capture starts as soon as interface works) incl. usage of the index.
|M4.29 - CDM SDD output optimised for Xper2||D4.1 - Scratchpad common access point||Yde de Jong||Fri, 30/11/2012||Completed||
Decription: CDM SDD output optimised for Xper2 Applet incl. caching mechanism for thumbnails and web service serving and applet reading compressed SDD.
Partner: BGBM & UPMC
|M4.30 - Integrating the biowikifarm into ViBRANT authentication||D4.2 - Ontology tools||Yde de Jong||Fri, 30/11/2012||Completed||
Description: In order to make a cross-cutting editing between ViBRANT-Scratchpad and ViBRANT-biowikifarm users practical, a joint authentication system needs to be established. This will require the collaboration with WP1, JKI has little expertise in this area.
Deadline: 30 November 2012
|M5.28 - Implement enhanced user interface tools for managing keys in Scratchpads||D5.3 - Sustainable software services||Gregor Hagedorn||Fri, 30/11/2012||Completed|
|M5.34 – Land cover classification tool||D5.2 - Functional tools||Neil Caithness||Fri, 30/11/2012||Completed||
The GlobCover Land Cover project (http://due.esrin.esa.int/globcover/) has released two global land cover classifications for the periods December 2004 - June 2006, and January - December 2009. These are the highest resolution (300 metres) global land cover products ever produced. The Land Cover service will deliver cover maps for the defined region and an analysis of the land cover change occurring in the region between 2005 and 2009. An extended analysis will also provide an array of patch statistics using the FRAGSTATS analysis package (http://www.umass.edu/landeco/research/fragstats/fragstats.html).
|M6.15 - Sample papers testing the XML-based editorial workflow elaborated and published||D6.3 - Data publication workflow||Lyubomir Penev||Fri, 30/11/2012||Completed||
Original target: 31 May 2012
This milestone describes the existing XML schemas for submission of manuscript from Scratchpads to ZooKeys and the progress being that has been made in regard of their improvement. Milestone delayed by the decision to expand functionality of the Pensoft Writing Tool (PWT) to support the new Biodiversity Data Journal. Although PWT is fully operational in beta version at the time of writing this explanation note, the public test is expected to happen in February-March 2013 when not only PWT but also BDJ the publishing workflow will be fully operational. The test will be based on a automated export from Scratchpads to PWT API and published in Biodiversity data Journal.
|M6.16 - Refinements to XML-based workflow for peer-review based on user feedback||D6.3 - Data publication workflow||Lyubomir Penev||Fri, 30/11/2012||Completed||
Based on the analysis of three online surveys, the authoring and editorial processes of the Biodiversity Data Journal have been significantly refined. In addition to several purely technical suggestions for improvement, some brand new features, such as Community and Public review processes were implemented into the system. The scope of BDJ and the general workflow, from generation of manuscript in PWT to submission and publication to the Biodiversity Data Journal and dissemination of the published in BDJ content have been elaborated.
|D4.2 - Ontology tools||D1.1 - Overall Management||Yde de Jong||Mon, 31/12/2012||Completed||
http://vbrant.eu/sites/vbrant.eu/files/ViBRANT_D4.2b — Ontology Tools- Status report 2012.pdf
Develop the GBIF ontology tool and produce an equivalent tool based on a semantic wiki. Deliver a single user interface for ontology creation and editing based on user-acceptance of the alternative technologies.
Partners: GBIF (KOS) & JKI (Wiki's)
|M1.34 - Circulation of next meeting agenda||D1.1 - Overall Management||Dave Roberts||Mon, 31/12/2012||Completed|
|M1.35 - Second year financial reports||D1.1 - Overall Management||Dave Roberts||Mon, 31/12/2012||Completed|
|M5.29 - Implement application specific wrappers (bioclimatic modelling)||D5.3 - Sustainable software services||Neil Caithness||Mon, 31/12/2012||Completed||
An application specific wrapper for MaxEnt (http://www.cs.princeton.edu/~schapire/maxent/) has been implemented and can be seen working in the Vulnerability layer of the LEFT service on OBOE (https://oboe.oerc.ox.ac.uk/jobs/new/left).
A generic service for Species Distribution Modelling (SDM) that uses the wrapper for analysing user supplied data points will be released soon. I am attending the BioVel workshop on ENM in Stockholm on 16-17 January and will finalise the implementation of the service soon after the workshop. At the workshop I will discuss the requirements for making the OBOE SDM service available for execution in BioVel/Taverna workflows.
(Final comment and update: This collaboration with BioVel was not carried through. It seems that pressures within the two projects prevented an actual joining of effort, though I'd not rule this out for the future. NC, 27/11/2013)
|M1.36 - Second year annual progress report||D1.1 - Overall Management||Dave Roberts||Thu, 31/01/2013||Completed|
|M4.31 - Webservice-Layer adapted for ViBRANT||D4.1 - Scratchpad common access point||Yde de Jong||Thu, 31/01/2013||Completed||
Description: The CDM Web Service Interface will expose the indexed data to any third party developer.
|M4.32 - Integrating a wiki-glossary into the scratchpad||D4.3 - Design of robust services||Yde de Jong||Thu, 31/01/2013||Completed||
Description: A first demo of integrating a wiki-glossary into the scratchpad matrix editor should be available at the end of the year.
|M1.37 - Minutes of management committee meetings||D1.1 - Overall Management||Dave Roberts||Thu, 28/02/2013||Completed|
|M1.38 - Minutes of strategic board meetings||D1.1 - Overall Management||Dave Roberts||Thu, 28/02/2013||Completed|
|M4.22 - BiolFlor Data as semantic web||D4.2 - Ontology tools||Yde de Jong||Thu, 28/02/2013||Completed||
Description: In collaboration with the UFZ in Leipzig, create a German-Language demo of the large biolFlor property dataset, presently in a relational database and usable only as "onscreen" content, making it part of the semantic web.
Original Deadline: 30 Aug 2012
By the original deadline, we had the full biolflor data in a local database, analyzed and ready to go. The mapping to semantic representation is unfinished, however, and from work done thus far would benefit from greater use of skos approaches. Also more needs to be borrowed from skos for the purposes of tdwg (DwC uses none of skos). This extension of the milestone will require additional time.
Comment Yde: New version of BioFlor not available yet. An update is needed because 20% of the data are changed. JKI will start finishing this deliverable when a new version of BiolFlor will be ready.
I am aware that we could not finish the biolflor data milestoen. We had been waiting for an update to the nomenclature, which was delayed several months and reached us only in November. This is not part of the biolflor dataset properly, it is a separate dataset of the updated plant taxonomy, since the creation of the biolflor data, which are based on the standard list of 1998, almost 10% of the 3600 species in Germany had systematic or name changes. It does not make sense today to publish the semantics of the old taxonomy, so we are merging these data.
We are working hard on bringing this together, and I had hoped to finish it by end of 2012 as I wrote to Yde, but in fact it is dragging on, part due to the other work. I would appreciate if we can delay the milestone one more time to the end of January.
We did a small step. The “Dictionary of Invertebrate Zoology“ http://species-id.net/zooterms/ is now ready but it's a small step towards completion. Andreas.
|M5.30 - Implement biodiversity indices tool||D5.3 - Sustainable software services||Javier de la Torre||Thu, 28/02/2013||Completed||
The BICT service available on OBOE implements marine biodiversity indices with algorithms coded by WP8. For M5.30 we will use the same basic framework and implement the terrestrial indices identified by M5.22.
|M5.35 – Environmental variables tool||D5.2 - Functional tools||Neil Caithness||Thu, 28/02/2013||Completed||
The WorldClim (http://www.worldclim.org/) data sets provide a rich set of climate variables at high resolution (30 arc-seconds to 10 arc-minutes). This service will deliver climate variable maps for the defined region, along with summary climate diagrams and downloadable files for the region at specified subsampled resolutions.
The CDE - Climate Data Extractor service is complete and an example run can be downloaded here:
|M8.22 - Prototype version of a start-up portal for discovery of GBIF mediated data||D8.3 - A start-up portal for discovery of GBIF mediated data||Olaf Bánki||Fri, 01/03/2013||Completed||
The GBIF Secretariat has developed a first version of the Nodes Portal Toolkit Startup that is focused on providing GBIF country Participant Nodes with a initial national biodiversity information site as web presence. The first version of the NPT Startup is currently send out for review with a deadline for feedback within the GBIF community up to 6 May 2013.
Read here about the materials that accompany this review:
|M5.31 - Review of target applications and services (molecular identification)||D5.3 - Sustainable software services||Neil Caithness||Sun, 31/03/2013||Completed||
The molecular data identification service will use a number of 3rd part tools and services: NCBI BLAST, and the Barcode of Life Database (BOLD). This new service will provide taxon identifications of DNA sequences using the EMBL and BOLD reference databases that contain validated reference sequences of known taxa. M5.31 is a review of the APIs for these 3rd part services to ensure suitability for the implementation of the identification service integrated into the OBOE framework.
|M6.17 - New open access data publishing journal||D6.3 - Data publication workflow||Lyubomir Penev||Sun, 31/03/2013||Completed||
The present milestone describes the focus, scope and policies of the Biodiversity Data Journal (http://biodiversitydatajournal.com).
|M8.25 - Scientific document on new horizons in taxonomic data publishing||D8.1 - Scratchpad modules engaging citizen scientists||Christos Arvanitidis||Sun, 31/03/2013||Completed||
M8.25 - Scientific document on new horizons in taxonomic data publishing (micro-CT tomograms, in collaboration with WP6) (month 28, HCMR). This document will demonstrate the potential as well as the new opportunities opening by the publication of micro-CT tomograms and their possible exploration by the reader/user. The consequences of this type of publication on the current system of type material deposition and its loaning system from the Museums will be presented and discussed in detail.
|M1.40 - Circulation of next meeting agenda||D1.1 - Overall Management||Dave Roberts||Tue, 30/04/2013||Completed|
|D2.3 - Financial sustainability||D1.1 - Overall Management||Dave Roberts||Fri, 31/05/2013||Completed||
Report on options for the ViBRANT financial sustainability model including selection of preferred model and accompanying Service Level Agreements (SLA's).
|M2.15 - Biodiversity data citation metric||D6.3 - Data publication workflow||Simon Rycroft||Fri, 31/05/2013||Completed||
Meeting and discussion group established to consider options for a biodiversity data citation metric for data published through the ViBRANT network
This has been pushed back, and combined with M2.19, as there is significant overlap between the two milestones.
|M2.19 - Report on the options for a biodiversity data citation metric for data published through ViBRANT||D6.3 - Data publication workflow||Simon Rycroft||Fri, 31/05/2013||Completed||
This report will detail the options available to ViBRANT to enable the assessment of an individual's contributions to a project and the impact of those contributions. An initial test case will be developed using the Scratchpads, with the principals being valid for all mechanisms of publishing data from ViBRANT, and also to non-ViBRANT projects.
|M4.33 - XML Tranformations CDM export||D4.3 - Design of robust services||Yde de Jong||Fri, 31/05/2013||Completed||
Description: Write XSL transformations to transfer CDM publishing output to MediaWiki.
|M1.39 - Organise final meeting||D1.1 - Overall Management||Dave Roberts||Sun, 30/06/2013||Completed||
Original target date was 31 March 2013 for this milestone. The meeting is now planned as a joint conference with several other projects and will take place in Rome in September. The venue is being organised by our colleagues in LifeWatch. A draft programme exists, but is not published pending the confirmation of venue and date.
Milestone is deferred to 30 June 2013
|M1.41 - Minutes of management committee meetings||D1.1 - Overall Management||Dave Roberts||Sun, 30/06/2013||Completed|
|M1.42 - Minutes of strategic board meetings||D1.1 - Overall Management||Dave Roberts||Sun, 30/06/2013||Completed|
|M4.35 - Filter functionality CDM export||D4.1 - Scratchpad common access point||Yde de Jong||Sun, 30/06/2013||Completed||
Description: Filter functionality implemented. Implementation of filter functionality in csv export from CDM to provide filtered checklist data in scratchpads.
|M4.36 - XPer2-CDM-relation for taxonomic hierarchy specification||D4.1 - Scratchpad common access point||Yde de Jong||Sun, 30/06/2013||Completed||
Description: Modify the taxonomic management in Xper2 using the standard mechanism for taxonomic hierarchies in the CDM and Scratchpads.
Partners: BGBM & UPMC
|M2.18 - Data search portal providing a single point of entry to all Scratchpad data completed||D5.3 - Sustainable software services||Walter Berendsohn||Wed, 31/07/2013||Completed||
A data search portal will allow external projects to easily access the data from all indexed Scratchpads, without having to know about each individual Scratchpad, and without having to access each one individually. The portal will also assist data providers to clean up the data and help de-duplicating and unifying it.
Note: Due date changed from 31/05/13 to 31/07/13 as BGBM had multiple deadlines in WP4 occuring on the same date (Lorna - discussed on Skype with Simon).
|M3.15 Ambassadors network is fully operational||D3.3 - Community delivery and evaluation||Thierry Backeljau||Wed, 31/07/2013||Completed||
State of the art of the Ambassadors network is given and a mechanism for long-term sustainability of the Scratchpads community support is established.
|M4.34 - Prototype for taxonomic generalisation||D4.1 - Scratchpad common access point||Yde de Jong||Wed, 31/07/2013||Completed||
Description: Specification for the methodology for the generalisation of descriptive data (e.g. from specimens to taxon) and provide a prototype implementation in Xper2
Partner: UPMC (exact delevery date to be defined)
2 April 2013:
We began to develop some structures which will be useful to store taxonomic generalisation. We are testing these new pieces of software. So we propose the end of july for the M4.34 - Prototype for taxonomic generalisation. I hope it is OK for your point of view.
|M7.19 - Review of pilot of reference de-duplication software||D7.3 - Literature search||Dauvit King||Wed, 31/07/2013||Completed||
Working with community contributed references to RefBank means that our repository will have a large number of duplicate references arising from:
We consider it important to RefBank’s success that there are as few blocks as possible to user contributions: users should simply upload references as they are without having to specially reformat them to suit RefBank. This design decision leads to the problem of multiple references; however, we consider it preferable that the duplicates are resolved within RefBank rather than prevent the loading of these references at all, so hindering the workflow of our potential contributors.
The problem of de-duplication is still unresolved within bibliographic reference management. We will need to develop a tool to automatically identify canonical forms of a reference from the many references loaded into RefBank. Our approach is based on graph theory, with each reference forming a node in a graph and the emergent centroid being considered the canonical form. Various algorithms will be used to calculate the centroid, decomposing the reference so that the most appropriate algorithm can be used, for example Jaro-Winkler for author names. This canonical form of a reference will be returned in future searches, however, the other references will not be deleted but simply marked as unavailable to general searches. Manual curation will be enabled so that a user can override RefBank’s canonical form if necessary.
|M8.21 - Integration of visualization applications with Scratchpads||D8.2 - Analytical and reporting tools||Javier de la Torre||Wed, 31/07/2013||Completed||
Integration of visualization applications with Scratchpads
This has been delayed because of the migration from Drupal 6 to 7. A workshop on data visualization using CartoDB/GeocAT has been organized in November in which developers from WP2 and WP8 have envision where
|M8.23: Integration of the 3D morphological and anatomical data in Scratchpads||D8.1 - Scratchpad modules engaging citizen scientists||Christos Arvanitidis||Wed, 31/07/2013||Completed||
To enhance the potential of Scratchpads in publishing micro-CT tomograms through which the user will have a much more complete access to both morphological and anatomical characters.
|M1.43 - Circulation of next meeting agenda||D1.1 - Overall Management||Dave Roberts||Sat, 31/08/2013||Completed|
|M6.18 - Testing automated tools of dissemination of published results to aggregators and indexing services||D6.3 - Data publication workflow||Lyubomir Penev||Sat, 31/08/2013||Completed||
The milestone forms part of D6.3 and presents the results of testing of automated tools to export sub-article level content into Darwin Core Archive and Taxon X formats.
|M8.18 - Scratchpads module for data recording (Citizen Science ) - Alpha version||D8.1 - Scratchpad modules engaging citizen scientists||Christos Arvanitidis||Sat, 31/08/2013||Completed||
Scratchpads module for data recording (Citizen Science ) - Alpha version
The delivery of this Milestone was postponed from the first semester of the third year of the project because it needs more time for collaboration with WP2. Migration from Drupal6 to Scratchpads2 requires additional effort both from WP8 and WP2 to deliver the Alpha version of the data recording module.
Alpha version is almost there. Needs a little work from NHM team. However, it is postponed in order to integrate the apps for the mobile phones.
|M8.20 - Ecological and conservation applications implemented as a service||D5.2 - Functional tools||Christos Arvanitidis||Sat, 31/08/2013||Completed||
Ecological and conservation applications implemented as a service
The Biological Index Calculation Tool (BICT) is an online tool available via OBOE (Oxford Batch Operation Engine, https://oboe.oerc.ox.ac.uk/). BICT calculates up to nine different biodiversity indices on data submitted by the user and returns calculated data as well as a graphical report.
The service is almost there. However, it is postponed because ther will be an effort to integrate more indices which will subsequently be used for the activities of the EMBOS (European Marine Biodiversity Observation System; COST project) network which start next fall.
|M8.24: Scientific document with the results from the COMBER data||D8.1 - Scratchpad modules engaging citizen scientists||Christos Arvanitidis||Sat, 31/08/2013||Completed||
A summary of the scientific results of the two years of operation of the COMBER pilot project. The results of the testing of the primary scientific hypothesis will also be provided.
It is postponed because more analysis is needed.
|M4.26 - Joint conference with LifeWatch and other FP7 projects||D1.1 - Overall Management||Yde de Jong||Fri, 06/09/2013||Completed||
Contribute to joint conference with LifeWatch and other FP7 projects in Italy (2-6 September 2013).
Letter to Nature: http://www.nature.com/nature/journal/v502/n7470/full/502171d.html
Partner: UvA & RBINS
|M4.37 - Xper2 and EDIT Platform publishing capability on Mediawiki||D4.3 - Design of robust services||Yde de Jong||Mon, 30/09/2013||Completed||
Description: Implementation of MediaWiki as a versioned publication tool for long-term availability of online published content from Scratchpad, Platform, and Xper2 implementations.
Partner:UPMC & BGBM
Deadline: 31 May 2013
|M4.43 - Global Names Europe||D4.3 - Design of robust services||Yde de Jong||Tue, 15/10/2013||Completed||
Contributing to the Global Names Architecture developments as a necessary component of Research Data e-Infrastructures: Framework for Action in H2020
|D7.3 - Literature search||D1.1 - Overall Management||Dauvit King||Thu, 31/10/2013||Completed||
This, the third and final deliverable of workpackage seven, was originally conceived of as an "Enhanced search facility to locate concepts based on linguistics and proximity rules." It was superseded during the project by the need to provide a breadth of coverage to enable a bibliography of life.
The bibliography of life can be accessed at http://biblife.org/.
|M1.44 - Minutes of management committee meetings||D1.1 - Overall Management||Dave Roberts||Thu, 31/10/2013||Completed|
|M3.17 Suggestions for potential new user groups||D3.3 - Community delivery and evaluation||Peter van den B...||Thu, 31/10/2013||Completed||
Work towards a better understanding of the diffuse user community for biodiversity informatics. Look at changes that occur in the behaviour as people start using Scratchpads and sharing their work through these new technologies.
|M4.38 - ZooKeys special issue on Fauna Europaea data papers||D4.1 - Scratchpad common access point||Yde de Jong||Thu, 31/10/2013||Completed||
M4.38a – Migration of FaEu production server. Partners: UvA, MfN (established: http://www.faunaeur.org)
State of affairs 1 July 2013:
|M4.40 - Advanced Statistics web services for the ViBRANT Index||D4.3 - Design of robust services||Yde de Jong||Thu, 31/10/2013||Completed||
Advanced Statistics web services in the ViBRANT Index (e.g. to search and count objects within single classifications or even sub-trees)
|M7.20 - Workpackage software documentation produced||D7.3 - Literature search||Dauvit King||Thu, 31/10/2013||Completed||
To encourage uptake and use, and for future enhancement and maintenance after completion of ViBRANT, all workpackage produced software must be fully documented to consistent quality, informed by the appropriate standards.
|M7.26 – Workpackage software packaged||D7.3 - Literature search||Dauvit King||Thu, 31/10/2013||Completed||
For sustainability and to formalise our contractual agreement with the EC, we need to package the software in industry standard formats, following accepted coding conventions and using version control. Software to be deposited in the Scratchpads git repository.
|M7.27 – Publish ViBRANT NLP corpus||D7.2 - Mark-up modules||Dauvit King||Thu, 31/10/2013||Completed||
To develop, refine and assess our data mining work, and the similar work of others aiming to mine biodiversity texts, a substantial gold standard corpus is required. None currently exists. This milestone addresses the community need.
|M3.18 Platform for Cybertaxonomy workshop in Berlin||D3.3 - Community delivery and evaluation||Thierry Backeljau||Mon, 11/11/2013||Completed||
In several meetings with European taxonomists (e.g. in Leiden and Berlin, Feb 13) the need for an in depth training in usage of the EDIT Platform tools was expressed. The workshop will be attended by taxonomists from Austria, Belgium, England, Finland, France, Germany, Greece, Italy, Scotland, Spain, and The Netherlands. It feeds into WP3 tasks 3.1.C and 3.2.A in the ViBRANT Workplan.
Responsible partners: BGBM, UPMC
|M5.32 - Tests and validation of the services in coordination with Workpackage 3||D5.3 - Sustainable software services||Neil Caithness||Fri, 15/11/2013||Completed||
We will conduct a phase of evaluationand feedback on OBOE services in close cooperation with WP3 (Training, outreach and community support). We wish to ensure that the services are presented in a consistent and appropriate manner for target user community. WP3 is best positioned to carry out these evaluations.
|M5.36 – Pipeline tool for species distribution modelling||D5.2 - Functional tools||Neil Caithness||Wed, 27/11/2013||Completed||
The SDM service implements the common pipeline as follows: 1) enter specimen locality coordinates, 2) collate environmental data records for the set of locality coordinates, 3) calculate an SDM, 4) project the SDM into the user specified region of interest, 5) for multiple species models calculate additive surfaces for alpha diversity, also called stacked SDMs. See: https://oboe.oerc.ox.ac.uk/
|M5.40 – Sustainable services. Completion of the documentation of services for D5.3||D5.3 - Sustainable software services||Neil Caithness||Wed, 27/11/2013||Completed||
1) Full documentation for the OBOE API is available here: https://oboe.oerc.ox.ac.uk/docs
|M7.18 - First integration phase complete||D7.3 - Literature search||Dauvit King||Wed, 27/11/2013||Completed||
The bibliography service integrations is achieved through a Scratchpads-to-RefBank harvester program.
The mark-up modules integration is achieved through the standard OBOE interface.
See the milestone report for implementation details and sustainability after ViBRANT.
The original DoW submitted in 2010 gave a target date of 31 March 2013 for this milestone. For various reasons the milestone reporting date was rescheduled on several occasions. These changes are fully documented in the milestone report.
The milestone was finally confirmed as achieved in full on Wednesday 27 November 2013, though some components of it has been in place for over six months by then.
|D5.3 - Sustainable software services||D1.1 - Overall Management||Neil Caithness||Fri, 29/11/2013||Completed||
Refined and sustainable software services available for public use with mechanisms to measure usage rates.
|D1.1 - Overall Management||D1.1 - Overall Management||Dave Roberts||Sat, 30/11/2013||Completed|
|D2.4 - Unit testing||D1.1 - Overall Management||Simon Rycroft||Sat, 30/11/2013||Completed||
Distributed and automated unit testing mechanism for Scratchpad code completed and available. This will operate in conjunction with the Scratchpad Sandbox to ensure that the latest version of the software is available for testing.
|D3.3 - Community delivery and evaluation||D1.1 - Overall Management||Thierry Backeljau||Sat, 30/11/2013||Completed||
Assessment of a self supporting open source community for sustainable implementation of the ViBRANT consortium and the integrated Virtual Research Environment
|D4.3 - Design of robust services||D1.1 - Overall Management||Yde de Jong||Sat, 30/11/2013||Completed||
Develop robust services, based on usage statistics and user feedback, that enhance the prototype tools delivered under D4.1 & D4.2
|D6.3 - Data publication workflow||D1.1 - Overall Management||Lyubomir Penev||Sat, 30/11/2013||Completed||
The present deliverable describes several workflows and tools developed or upgraded by Pensoft in the course of the ViBRANT project. These include: (1) Data and narrative (text) integrated publishing workflow of the Biodiversity Data Journal (BDJ); (2) The upfront markup data publishing Pensoft Writing Tool (PWT); (3) Data paper workflow developed by GBIF and Pensoft; (4) Markup and export of atomized content from journal articles, such as taxon treatments, names, primary biodiversity data and bibliographic references; (5) journal-to-wiki simultaneous publishing workflow; (6) Large data species description using ISA TAB metadata standard.
|D8.3 - A start-up portal for discovery of GBIF mediated data||D1.1 - Overall Management||Olaf Bánki||Sat, 30/11/2013||Completed||
The Nodes Portal Toolkit (NPT) Startup enables countries to establish a web presence with relevant biodiversity information from GBIF and EOL. The NPT Startup will be built on the ScratchPads platform, and will extend developments of ViBRANT to a broader context of the use of biodiversity data portals. The first version of the Nodes Portal Toolkit (NPT) Startup will be available as a Drupal profile accompanied with relevant documentation for use and further development. The NPT will be deployed in several countries within and outside Europe. At the completion of this deliverable, there will also be some commitments from the GBIF network to further develop the NPT Startup with more advanced functionalities.
|M2.20 - Ongoing module development supporting prioritised features requested by users through WP3||D5.3 - Sustainable software services||Simon Rycroft||Sat, 30/11/2013||Completed||
Additional Scratchpads features that are requested through the Scratchpads Issues queue (http://support.scratchpads.eu) are prioritised by WP3 and then ordered based on the priority and estimated development time. These additional features will then be developed in the order specified.
|M3.16 Established user support services to keep the open source network community alive and vibrant||D3.3 - Community delivery and evaluation||Thierry Backeljau||Sat, 30/11/2013||Completed||
Established support systems and their sustainability post-VIBRANT are discussed.
|M1.45 - Third year annual progress report||D1.1 - Overall Management||Dave Roberts||Wed, 15/01/2014||Completed|
|M1.46 - Third year financial reports||D1.1 - Overall Management||Dave Roberts||Wed, 29/01/2014||Completed|