Identification of specimens and observations is a crucial task . Today
methods are based on molecular sequences (barcoding), image or sonogram
analysis, morphometry, or morphological data. For this last type of data, which
is also the most often available information, we use identification keys. Since
the first printed key published by Lamark (Flore Francoise 1778) taxonomists
have developed various forms of « identification keys » :
single-access, free-access and multi-entry keys (Hagedorn, 2010).

In this document we make a short review of existing key construction software for these three
types of keys, and then we describe the architecture and workflow to offer such
webservices linked to Scratchpads and the CDM.

A few comments:

1. Many attempts to contact the Lattice project (http://lattice.umiacs.umd.edu/) have met with no response.
2. Likewise, attempts to contact LIRMM (http://www.phylogeny.fr/version2_cgi/simple_phylogeny.cgi) has also been unsuccessful.
3. The Lisbeth software (http://lis-upmc.snv.jussieu.fr/lis/?q=en/resources/software/lisbeth) is not yet available for Unix platforms, though as OBOE now includes Windows VMs as available platforms running Lisbeth as a service can be reinvestigated.

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.

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

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

The platform requirements review has been superseded by full implementation for services on both Unix and Windows systems. 

The OBOE system now consists of at least nine machines:

1. Unix physical machines (Vibrant, Bonnacon, Cockatrice, Karakal)
2. Unix virtual machines (Goblin, Voonith)
3. Windows physical machines (Gecko)
4. Windows virtual machines (Nyogtha, Syncerus)

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.

A short decsription of the prototype of the publishing module, including screenshots of the steps.

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.

For accessing existing ontology resources within Scratchpad sites

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.

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.

These support biodiversity inventory and monitoring programs

Scratchpads user support systems are analysed and discussed. Results of a maintainer survey will feed into the development and project management of Scratchpads.

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.

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)

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).

Slide show presented in TDWG Conference (geospatial before and after on slides 8/9, taxonomic before and after are on slides 10 and 12)

Paper describing the COMBER project

Description: Prepare scoping document on a KOS architecture for the GBIF network including the requirements for a new ontology
tool to provide a new GBIF Glossary of Terms used in Biodiversity Informatics.

Partner: GBIF

Deadline: First draft scoping document finalized by 31 December 2011

http://vbrant.eu/content/m417-extensions-dwc-export-functionality

No strategic board meeting has been called.

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).

Partner: BGBM

Metadata and processing code added to RefBank to cover origin of bibliographies.

Use cases:
1) Bibliographies taken from a publication, in which case the origin is the bibliographic details of the original publication or (possibly) RefBank ID of original publication, which will be accurate but not human-user friendly.
2) Bibliographies contributed by a particular author, in which case, attribution of the bibliography is appropriate.
3) Bibliographies harvested from, or contributed by, existing resources such as ITIS, in which case the contributor is the short name of the existing bibliographic resource.

These ideas of origin could also be extended to attribute contributions made by people editing a reference.

This milestone was defined in M7.15.

Description: Develop a new prototype (GBIF) Glossary of Terms registry for terms used by the ViBRANT and GBIF infrastructure.

Partner: GBIF

Deadline: April 2012

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.

Partner: JKI

Original Deadline: 31 March 2012

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.
Brought forward to Friday 1 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 M7.16 and M7.24.

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.

Description:  User interface for flexible mapping of Scratchpad 2 to DwC-A

Partner: BGBM

Description: Pilot deployment of the ViBRANT Single Access Key Service in the Platform (Hackaton)

Partners: BGBM & UPMC

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.

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.

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++).

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.

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.

Release of functional tools as products accessible through the API.

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.
Finally it is included a review of the current usage of the two applications and possible ways of continuing the work.

Download image

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.

Partner: BGBM

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.

Partner: JKI

Deadline: 30 November 2012

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).

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.

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)

Description: The CDM Web Service Interface will expose the indexed data to any third party developer.

Partner: BGBM

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.

Date: 30/11/2012

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.

Date: 09/10/2013

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.

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:
http://oboe.oerc.ox.ac.uk/download/514b2093c0de6b46500009de

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.

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.

Report on options for the ViBRANT financial sustainability model including selection of preferred model and accompanying Service Level Agreements (SLA's).

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.

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

Description: Modify the taxonomic management in Xper2 using the standard mechanism for taxonomic hierarchies in the CDM and Scratchpads.

Partners: BGBM & UPMC

State of the art of the Ambassadors network is given and a mechanism for long-term sustainability of the Scratchpads community support is established.

Working with community contributed references to RefBank means that our repository will have a large number of duplicate references arising from:

• letting users load textual, as opposed to marked-up, references which means that a reference can be entered using any style such as Harvard, Chicago, etc laid out in the published source.
• near identical references varying only by a comma or space caused by individual stylistic quirks of the contributors.
• near identical references varying only typographical errors, whether in the original source or induced later through re-keying the reference.

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.

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.

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.

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 routines are made available by OBOE (https://oboe.oerc.ox.ac.uk/; under the BICT tool), which already provides the interface to other ViBRANT services. This was decided in order to avoid having multiple ways and services through which the calculation routines would be made available. Scripts for the calculation of the indices, as well as templates for input and output formats have been delivered to WP5 leader, written in C++.

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.

Contribute to joint conference with LifeWatch and other FP7 projects in Italy (2-6 September 2013).

Conference: http://conference.lifewatch.unisalento.it/index.php/EBIC/BIH2013

BIHorizon: http://h2020.myspecies.info/

Letter to Nature: http://www.nature.com/nature/journal/v502/n7470/full/502171d.html

Partner: UvA & RBINS

Contributing to the Global Names Architecture developments as a necessary component of Research Data e-Infrastructures: Framework for Action in H2020

M4.38a – Migration of FaEu production server. Partners: UvA, MfN (established: http://www.faunaeur.org)
M4.38b – New version of FaEu. Partner: UvA (second beta at: http://faunaprod.uva.sara.nl/index.php). Final version released at 9 April 2013.
M4.38c – FaEu data papers as ZooKeys special issue. Partner: UvA, Pensoft

State of affairs 1 July 2013:
- 58 data papers in preparation in Pensoft Writing Tool
- 3 descriptive ZooKeys papers in draft for special issue
- 3 vision ZooKeys papers in preparation for special issue

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.

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.

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.

1) Full documentation for the OBOE API is available here: https://oboe.oerc.ox.ac.uk/docs
2) Source code and associated documentation for the OBOE system and all services is maintained on a version control system at the OeRC and is available on request.

Refined and sustainable software services available for public use with mechanisms to measure usage rates.

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.

Develop robust services, based on usage statistics and user feedback, that enhance the prototype tools delivered under D4.1 & D4.2

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.

Established support systems and their sustainability post-VIBRANT are discussed.