Moving from Physical to Digital Collections: JRA Outputs
Open source software that can recognise, process and annotate images that contain multiple specimens (e.g. whole drawer scans of
pinned insects or slide arrays) has been developed.
A workshop was held in September 2014 to develop a specification and produce a functional software prototype called Inselect.
Optimal Automated Metadata Capture
This aspect of the SYNTHESYS3 JRA focused on the development of software that is able to automatically identify properties of an image without human intervention, and capture easily searchable information that can be integrated into virtual Natural History Collections.
This research was divided into four ‘sections':
1. Review of development of tools and workflows which incorporate automatic or semi-automatic metadata capture using Optical Character Recognition (OCR)
2. Review of development of Natural Language Processing (NLP) for parsing OCR text into Darwin core fields
3. Review of Handwritten Text Recognition (HTR) and (semi) automatic specimen image classification.
4. Review of automatic capture of character including colour, shape as well as exif data.
You can read the executive summary and full report here (deliverable 4.2)
Outputs from the SYNTHESYS2 Access visits can be viewed here.
Collections Management Standards: Networking Activity 2 outputs
A set of performance indicators (PIs) for collections management have been developed (Deliverable 2.2). These aim to provide a set of benchmarks and definitions that are transferable across institutions, allowing individual bodies to create their own internal subsets of indicators. The SYNTHESYS project, with the help of a workshop held in October 2011, has developed a total of 68 PIs, related to the following categories:
- Long term trends in collections
- Distinct collections management activities
- The level to which activities are performed
- The efficiency to which activities are performed
A report on SYNTHESYS performance indicators can be found here.
Workshops & Training Courses
As part of the initiative to develop an EU-wide set of competencies for collections management (Deliverable 2.10), a workshop was held at the Museum National d’histoire Naturelle in Paris to discuss how this may be achieved (Deliverable 2.3). This task was brought together with an NHM bid to the Leonardo Transfer of Innovation Programme, resulting in €285,000 being awarded to facilitate the development of a pilot competency framework between October 2013 and September 2015. A report from the workshop can be found here.
To prepare for the delivery of a number of collections management training courses, a ‘Training the Trainer’ workshop was held at the NHM in October 2011. Following this, five modular training courses on key collections management areas then took place between November 2011 and June 2013 (Deliverable 2.13-17) These were:
- Effective collections emergency planning and salvage
- Access to collections
- Molecular collections
- Basic collections techniques
A detailed report on all the above courses can be found here.
A web-based Collections Self-Assessment Tool has been developed and is now ready for use (Deliverable 2.5). To date, this has been completed by 44 institutions of which 14 have since been audited by an external team. As well as providing valuable data on collection management needs in Europe, this aims to aid institutions with important planning and management information. Click here to log in or register your institution. A report on the collections self-assessment tool and its usage (Deliverable 2.8) can be found here.
A collaborative collection manager’s website and forum has been developed with the joint support of SYNTHESYS and EDIT (European Distributed Institute of Taxonomy). This has been created as a sub-domain of the RMCA Cybertaxonomy portal and can be found at http://eu-com.cybertaxonomy.africamuseum.be
Consolidating the Information Network of European Natural History Collections: Networking Activity 3 outputs
Report: technical possibilities for the rationalisation of data capture (Deliverable 3.1 of the SYNTHESYS2 project).
NA 3 outcomes course to be integrated into NA2 (Deliverable 3.3).
Storage system specification report (Deliverable 3.4)
Reverse Wrapper software delivered (Deliverable 3.5).
Annotations Workflow in Collections (Deliverable 3.7).
Rich data progress report (Deliverable 3.8).
Update of European collection data in BCI report (Deliverable 3.9).
Usability of Specimen access system for taxonomists (Deliverable 3.10).
Interface changed according to results of usability report (Deliverable 3.11).
PrediCtoR software tool: JRA1 outputs
The site has been created and is available at http://thermal-age.eu (“Deliverable 4.1″ of the SYNTHESYS2 project).
To read more about the tool, and to see how the software has been refined, read the following report JRA1-Del.4.3 (“Deliverable 4.3″ of the SYNTHESYS2 project).
New Screening protocol for non-or minimal destructive analyses: JRA2 outputs
JRA2 investigated creation of DNA libraries to reduce the need to re-sample rare museum specimens by effectively immortalizing one DNA sample. Ancient skeletal material was used as the model as the DNA is often both highly degraded and in demand from users.
JRA2 has developed, tested, and optimized new protocols which used in combination with next generation sequencing technologies can be applicable to the degraded DNA found in museum and herbarium samples. In particular, protocols for the creation of DNA libraries out of both skeletal museum specimens and soil embedded archaeological remains and in-solution capture enrichment (capturing genomic regions of interest from a DNA sample prior to sequencing using magnetic beads) were investigated.
- Development of a library preparation protocol adopted to highly degraded DNA (Deliverable 5.4 of the SYNTHESYS2 project)
- Protocol delivered adopted to the characteristics of hominin aDNA (Deliverable 5.5)
- Protocol for the immortalization of aDNA libraries (Deliverable 5.6)
- Development of a showcase capture-NGS protocol (Deliverable 5.7)
- Report on the success rate of mtCapture protocols applied to various different museum and archaeological specimens (Deliverable 5.8)
- Final protocol for mitochondrial and nuclear capture enrichment (Deliverable 5.9)
MORDOR – Methods for Optimal Recovery of DNA from Osteological Remains: JRA3 outputs
The central direction of the work of JRA3 has been to develop a system for the use of very small samples (microsamples) in ancient DNA extraction from museum bone specimens.
Protocol for contamination free DNA extraction from human bone for subsequent 454 sequencing reported (Deliverable 6.2 of the SYNTHESYS2 project; incorporated in the JRA2 Protocols report)
Validated, optimal DNA extraction protocol for microsamples (Deliverable 6.4)
Plants/fungi optimised DNA Extraction Techniques: JRA4 outputs
Tiina Särkinen et al. (2012) How to Open the Treasure Chest? Optimising DNA Extraction from Herbarium Specimens (Deliverables 7.1 and 7.2 of the SYNTHESYS2 project).
Staats et al. (2011) DNA Damage in Plant Herbarium Tissue (Deliverables 7.3, 7.4 and 7.5).
Staats et al. (2013) Genomic Treasure Troves: Complete Genome Sequencing of Herbarium and Insect Museum Specimens (Deliverable 7.7).
Plant family-level herbarium DNA extraction database (HDED) (Deliverable 7.6).
Development of high-throughput methods for DNA isolation from invertebrates with muco-polysaccharide rich tissue: JRA5 outputs
Presentation of alternative method for DNA extraction from mucopolysaccharide rich tissue (Deliverable 8.1 of the SYNTHESYS2 project).
Complete extensive parallel testing in several institutions of safe high throughput method for DNA extraction from muco-polysaccharide rich tissue with notes on general applicability (Deliverable 8.4).