Moving Physical to Digital
This package improved access to data stored digitally within natural history collections by developing mechanisms that enabled institutions to enrich digital media with metadata to increase their usability to users.
Inselect is 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).
A workshop was held in September 2014. Read about Inselect in more detail.
Optimal Automated Metadata Capture
This aspect of SYNTHESYS3 research 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 .
SYNTHESYS3 consisted of 3 network packages - one of these was the project management package, led by the Natural History Museum, London.
The other two packages are as follows:
This developed collection management policies and strategic priorities for open and flexible access to virtual and new physical collections. It operated the Collections Self-Assessment Tool that was developed under SYNTHESYS 2.
NA3 ensured that SYNTHESYS3 outputs were utilised by the broader research and development community and that benefits created continued beyond the life of the project.
Outputs from the SYNTHESYS2 Access visits can be viewed here.
SYNTHESYS2 research assisted in meeting researcher demands for usable DNA from museum specimens by enhancing and improving extraction technology and protocols. It developed non-invasive tools for estimating the presence of ancient DNA and optimal extraction protocols in both ancient and recent specimens, through the following activities:
A novel decision-making software tool was developed to help collections managers and users to quantify the risks associated with destructive analysis of specimens.
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
We 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.
This 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.
(Methods for Optimal Recovery of DNA from Osteological Remains) Development of a system for ancient DNA extraction of very small samples from museum bone specimens.
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)
Optimised DNA extraction techniques from botanical specimens:
We developed protocols to overcome the masking effects of alcohol preservation, secondary compounds and the presence of cell walls in DNA extraction from plant and fungal collections, with a view to scale up eventually by automation.
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 methods for DNA isolation from invertebrates with muco-polysaccharide-rich tissue:
This included replacing time-consuming single sample extractions with a high throughput DNA isolation procedure and improving yield from old samples.
Presentation of alternative method for DNA extraction from mucopolysaccharide rich tissue (Deliverable 8.1 of the SYNTHESYS2 project).
Report on tested replacement component for β-mercaptoethanol (Deliverable 8.2).
Present protocol adapted to high-throughput methods (96-well format) (Deliverable 8.3).
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).
A set of performance indicators (PIs) for collections management were developed (Deliverable 2.2). These provided a set of benchmarks and definitions that were 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, developed a total of 68 PIs, related to the following categories:
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:
A detailed report on all the above courses can be found here.
A web-based Collections Self-Assessment Tool was developed and is now ready for use (Deliverable 2.5). To date, this has been completed by 18 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 was 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
Report: technical possibilities for the rationalisation of data capture (Deliverable 3.1 of the SYNTHESYS2 project).
Collection software on BD Tracker delivered (Deliverable 3.2).
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).
Sociological implications of virtual annotations report (Deliverable 3.6).
Annotation workflow in collections report (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).
Under the previous SYNTHESYS contract (FP6) there were five technical NAs. If you would like more information on the outcomes of these email firstname.lastname@example.org
NA B – Complementarity
NA C – Collections Standards
NA D – Developing and maintaining databases
NA E – Collections management for New Types of collections (i.e. Molecular)
NA F – Implementation of Novel and Physical Analytical Methods in collections