scholarly journals DaRWIN: An open source natural history collections data management system

2019 ◽  
Vol 3 ◽  
Author(s):  
Marielle Adam ◽  
Franck Theeten ◽  
Jean-Marc Herpers ◽  
Thomas Vandenberghe ◽  
Patrick Semal ◽  
...  
Keyword(s):  
Natural History ◽  
Open Source ◽  
Management System ◽  
Data Management System ◽  
Sensitive Information ◽  
Type Specimens ◽  
Natural History Collections ◽  
Access Rights ◽  
Different Levels ◽  
New Framework

DaRWIN (Data Research Warehouse Information Network) is an in-house solution developed by the Royal Belgian Institute of Natural Sciences (RBINS), as a Natural History collections management system for biological and geological samples in collections. In 2014, the Royal Museum for Central Africa (RMCA) adopted this system for its collections and started to take part in new developments. The DaRWIN database currently manages information on more than 600,000 records (about 4 million specimens) housed at the RBINS and more than 650,000 records (more than 1 million specimens) at the RMCA. DaRWIN is an open source system, consisting of a PostgreSQL database and a customizable web-interface based on the Symfony framework (https://symfony.com). DaRWIN is divided into 2 parts: one public section that gives a “read-only” access to digitised specimens, one section for registered users, with different levels of access rights (user, encoder, conservator and administrator), customizable for each collection and allowing update of specimens and collections, daily management of collections, and the potential for dealing with sensitive information. one public section that gives a “read-only” access to digitised specimens, one section for registered users, with different levels of access rights (user, encoder, conservator and administrator), customizable for each collection and allowing update of specimens and collections, daily management of collections, and the potential for dealing with sensitive information. DaRWIN stores sample data and related information such as place and date of collection, missions and collectors, identifiers, technicians involved, taxonomy, identification information (type, stage, state, etc.), bibliography, related files, storage, etc. Other features that deal with day-to-day curation operations are available: loans, printing of labels for storage, statistics and reporting. DaRWIN features its own JSON (JavaScript Object Notation) webservice for specimens and scientific names and can export data in tab-delimited, Excel, PDF and GeoJSON formats. More recently, a procedure for importing batches of data has been developed, based on tab-delimited files, making integration of data from (old/historical) databases faster and more controlled. Additional improvements of the user interface and database model have been made. For example, parallel taxonomical hierarchies can be created, allowing users to work with temporary taxonomies, old scientific names (basionyms and synonyms) and document the history of type specimens. Finally, quality control and data cleaning on several tables have been implemented, e.g. mapping of locality names with vocabularies like Geonames, adding ISO 3166 two-letter country codes (https://www.iso.org/iso-3166-country-codes.html), cleaning duplicates from people/institutions and taxonomy catalogues. A tool for checking taxonomical names on GBIF (Global Biodiversity Information Facility), WoRMS (World Register of Marine Species) and DaRWIN itself, based on webservices and tab-delimited files, has been developed. Last year, RBINS, RMCA and Meise Botanic Garden (MBG) defined a new framework of collaboration in the NaturalHeritage project (http://www.naturalheritage.be), in order to foster interoperability among their collection data sources. This new framework presents itself as one common research portal for data on natural history collections (from DaRWIN and other existing collection databases) of the three partnered institutions and makes data compliant to a standard agreed by the partners. See Poster "NaturalHeritage: Bridging Belgian Natural History Collections" for more information. DaRWIN is accessible online (http://darwin.naturalsciences.be). A Github repository is also available (https://github.com/naturalsciences/natural_heritage_darwin).

scholarly journals Symbiota2: Enabling greater collaboration and flexibility in mobilizing biodiversity data

2019 ◽  
Vol 3 ◽  
Author(s):  
Mary Barkworth ◽  
Benjamin Brandt ◽  
Curtis Dyreson ◽  
Neil Cobb ◽  
Will Pearse
Keyword(s):  
Natural History ◽  
Web Services ◽  
Management System ◽  
The United States ◽  
Content Management ◽  
Database Management System ◽  
Data Management System ◽  
Natural History Collections ◽  
A Site ◽  
Site Managers

Symbiota, the most used biodiversity content management system in the United States, has helped mobilize over 35 million specimen records from over 750 natural history collections via 40+ separate installations. Most Symbiota records come from natural history collections but some Symbiota instances also incorporate records from observations, images, publications, and gardens. Symbiota serves as both a data management system for entering, annotating, and cleaning occurrence data, images and associated specimen data (e.g., genetic sequences, images, publications) and as a primary aggregator/publisher for data stored in any database system that can export to a comma separated value (csv) file. Symbiota integrates and displays data and images from many resources in multiple formats, some of which appeal primarily to researchers, others to land managers, educators, and the general public. After nearly 20 years, Symbiota is going through a major software revision through Symbiota2, a US National Science Foundation-funded project. The broad goals of Symbiota2 are to make it easier for developers to add new functionality, to improve usability, and to help site managers administer a site. Symbiota2 will have a plugin-based architecture that will allow developers to encapsulate functionality in a plugin. Symbiota2 will improve usability by supporting off-line use, enabling Wordpress (content-managment system) integration, and having a customizable user interface. Symbiota2 will help site managers by simplifying installation and management of a site. The three-year project is on-going, but so far we have created a Symbiota2 GithHub repository and a Docker image with all the necessary components for installing, configuring, and running Symbiota2, an object relational mapping (ORM) of the tables in the database management system (DBMS), and web services to connect to the DBMS via the ORM. We used Doctrine 2 for the ORM and API-Platform for the web services. By the third quarter of 2019, we anticipate deploying the plugin framework to encourage developers to create new functionality for biodiversity content management.

UHF RFID proof of concept (POC) with open-source ILS at Universiti Sains Malaysia (USM) Libraries

2015 ◽  
Vol 49 (2) ◽  
pp. 135-150 ◽  
Author(s):  
JingHuey Khor ◽  
Widad Ismail ◽  
Mohd Nasir Md Rashid ◽  
A. Akla Wan Ismail ◽  
Muhammad Qayum Omar ◽  
...  
Keyword(s):  
Data Management ◽  
Open Source ◽  
Management System ◽  
Data Management System ◽  
Proof Of Concept ◽  
Rfid Technology ◽  
Uhf Rfid ◽  
Content Type ◽  
Library Automation ◽  
Detection Technologies

Purpose – Universiti Sains Malaysia (USM) uses different detection technologies and integrated library systems (ILS) at its four libraries located at different sites. Hence, ubiquitous data management system is required in the four libraries to enable real-time data sharing and tracking among the libraries. The paper aims to discuss these issues. Design/methodology/approach – Proof of concept is used to verify the performance of integration between different detection technologies including barcode, high frequency (HF) and ultra high frequency (UHF) radio frequency identification (RFID) as well as Integrated Library Management Utility (ILMU) and Koha ILSs. Five pilot tests are performed to investigate the speed of the borrowing and returning transactions, the efficiency of security gate to detect non-borrowed items, and the reliability of the ubiquitous data management system. Findings – The HF RFID technology and the proprietary library system have been used in many libraries. The current study proves that the integration of the UHF RFID technology and the Koha open-source ILS, which is named as Total Open-Source Library Automation Solution, can be a novel solution and can serve as a guide for other libraries. Originality/value – In the current phase of library data management system, it is common to integrate various technologies in improving the efficiency of the library system. But, the combination of Koha with UHF RFID into a single ILS for intra-library automation system has not been proven. This shows the importance of the proposed proven proof of concept that proves such integration is suitable to be implemented at USM libraries and other libraries.

scholarly journals Taxonomic changes resulting from a review of the types of Australian Anoplognathini (Coleoptera: Scarabaeidae: Rutelinae) housed in Swedish natural history collections

Zootaxa ◽  
2021 ◽  
Vol 4908 (2) ◽  
pp. 225-238
Author(s):  
MATTHIAS SEIDEL ◽  
CHRIS A.M. REID
Keyword(s):  
Natural History ◽  
The Other ◽  
Type Material ◽  
Type Specimens ◽  
Natural History Collections ◽  
New Synonym ◽  
Senior Synonym ◽  
Taxonomic Changes ◽  
First Time ◽  
Total Type

The type material of Australian Anoplognathini (Coleoptera: Scarabaeidae: Rutelinae) housed in Swedish natural history collections is reviewed, concerning three genera: Anoplognathus Leach, 1815, Amblyterus MacLeay, 1819, and Repsimus MacLeay, 1819. The species were described by G.J. Billberg, J.W. Dalman, L. Gyllenhal, C.J. Schönherr, O. Swartz, and C.P. Thunberg. The contemporary type material of W.S. MacLeay in the Macleay Museum, Sydney, is also examined as it has been overlooked by previous researchers. In total, type specimens for 12 species described between 1817 and 1822 were found in the Naturhistoriska Riksmuseet in Stockholm the Evolutionsmuseet in Uppsala and the Macleay Museum. Five of these species are valid: Anoplognathus brunnipennis, (Gyllenhal, 1817); A. olivieri (Schönherr & Dalman, 1817); A. porosus (Dalman, 1817); Amblyterus cicatricosus (Gyllenhal, 1817); and Repsimus manicatus (Swartz, 1817). The other seven species are junior synonyms, as follows (senior synonym first): A. brunnipennis = Rutela chloropyga Thunberg, 1822 (new synonym); A. olivieri = Rutela lacunosa Thunberg, 1822 (new synonym); A. viridiaeneus (Donovan, 1805) = A. latreillei (Schönherr & Gyllenhal, 1817); A. viriditarsus Leach, 1815 = Rutela analis Dalman, 1817; and R. manicatus = Anoplognathus brownii W.J. MacLeay, 1819 = A. dytiscoides W. J. MacLeay, 1819 = Rutela ruficollis Thunberg, 1822 (new synonym). Authorship of A. latreillei and A. olivieri is corrected, as noted above. Anoplognathus brunnipennis has been misidentified for the last 60 years at least, leading to the synonymy noted above. Anoplognathus flavipennis Boisduval, 1835 (revised status), is reinstated as the oldest available name for the misidentified A. brunnipennis and the types of A. flavipennis in the Muséum National d’Histoire Naturelle, Paris, are illustrated. Lectotypes are designated for: Anoplognathus brownii, A. flavipennis, A. dytiscoides, Melolontha cicatricosa, Rutela analis, R. brunnipennis, R. lacunosa, R. latreillei, R. manicata, R. olivieri, R. porosa, R. ruficollis, and R. chloropyga. Photographs of all type specimens examined are presented for the first time. 

scholarly journals Digitisation of private collections

2020 ◽  
Vol 6 ◽  
Author(s):  
Luc Willemse ◽  
Veljo Runnel ◽  
Hannu Saarenmaa ◽  
Ana Casino ◽  
Karsten Gödderz
Keyword(s):  
Natural History ◽  
Communication Strategy ◽  
Data Management System ◽  
Specific Knowledge ◽  
Management Tools ◽  
Data Infrastructure ◽  
Natural History Collections ◽  
Private Collection ◽  
Collection Data ◽  
Private Collections

Results are presented of a study investigating solutions and procedures to incorporate private natural history collections into the international collections data infrastructure. Results are based on pilot projects carried out in three European countries aimed at approaches on how to best motivate and equip citizen collectors for digitisation: 1) In Estonia, the approach was to outline tools for registering, digitising and publishing private collection data in the biodiversity data management system PlutoF. 2) In Finland, the functionality of FinBIF, a portal offering a popular Notebook Service for citizens to store observations has been expanded to include collection specimens related to a field gathering event. 3) In the Netherlands private collection owners were approached directly and asked to start digitising their collection using dedicated software, either by themselves or with the help of volunteers who were recruited specifically for this task. In addition to management tools, pilots also looked at motivation, persons undertaking the work, scope, planning, specific knowledge or skills required and the platform for online publication. Future ownership, legality of specimens residing in private collections and the use of unique identifiers are underexposed aspects effecting digitisation. Besides streamlining the overall process of digitising private collections and dealing with local, national or international challenges, developing a communication strategy is crucial in order to effectively distribute information and keep private collection owners aware of ongoing developments. Besides collection owners other stakeholders were identified and for each of them a roadmap is outlined aimed at further streamlining the data from private collections into the international infrastructure. In conclusion recommendations are presented based on challenges encountered during this task that are considered important to really make significant progress towards the overall accessibility of data stored in privately held natural history collections.

scholarly journals CLAIM MANAGEMENT FRAMEWORK UNDER FIDIC 2017: CONTRACTOR CLAIM SUBMISSION

2019 ◽  
Vol 7 (2) ◽  
pp. 170-179
Author(s):  
Ahmed El-Ghrory ◽  
Md. Nor Hayati Bin Tahir ◽  
Norain Binti Ismail
Keyword(s):  
Management System ◽  
Qualitative Methodology ◽  
Sensitive Information ◽  
User Friendliness ◽  
Management Framework ◽  
Different Levels ◽  
Management Issues ◽  
Claims Management ◽  
Centralized Database

Purpose of the study: The objective of this research is to develop a framework for managing the claim document. The contractual and management issues will be considered in this framework to enhance the Claims Management System (CMS). The framework includes the mechanism of claim submission based on the clauses and procedures of Fédération Internationale Des Ingénieurs Conseils (FIDIC, 2017). Methodology: Qualitative methodology has been selected for this paper as the topic requires a collection of sensitive information from an experienced professional. The proposed Claims Management (CM) framework is developed on the basis of a study conducted to rank the feature required for CMS. This study has been conducted among 43 experts in CM field working on contractor firm’s category A. Then, the framework was verified by seven experts who participated in the first study. Main Findings: Eleven features were required for CMS that can enhance contractor claim submission. These factors have different levels of importance. The top three factors are Tracking Claim Status (99.5%), Supporting all types of documents (96.3%), and having a Centralized Database (93.0%). Based on these features, the proposed framework was developed to improve contractor claim submission. Applications of this study: Applying the proposed framework reduces human efforts in getting documents related to claims by its systematic recording, transparency, reminder feature, contractual guide, user friendliness, and other features of the system. Moreover, it provides the contractual support pursuant to FIDIC 2017 clauses. Novelty/Originality of this study: The framework will improve contractor claim submission and the contractor will be satisfied by claim resolution and engineer determination. Side by side, the framework will save about 50% of time consumed (d is missing) by the claims analysts that is usually spent in collecting, screening, and identifying information related to claim event in the project’s documentation.

On some Type-specimens of Lepidoptera and Coleoptera in the Edinburgh Museum of Science and Art

1897 ◽  
Vol 21 ◽  
pp. 326-327 ◽  
Author(s):  
Percy Hall Grimshaw
Keyword(s):  
Natural History ◽  
New Genus ◽  
British Museum ◽  
Type Specimens ◽  
Histoire Naturelle ◽  
Science And Art ◽  
Natural History Collections ◽  
University Of Edinburgh ◽  
The University

The paper dealt with fifty-two species of butterflies and nineteen of beetles, the type-specimens of which had been discovered by the author in a collection purchased by the University of Edinburgh from M. Dufresne of Paris in the year 1819, and afterwards transferred to the Museum of Science and Art. In the case of the butterflies, the species referred to were described by Godart in the Encyclopédie Méthodique, while the beetles belonged to species described by Olivier in the same work, and also in his Histoire Naturelle des Insectes—Coléoptères, published about the same time. By the comparison of these original specimens with others in the Natural History Collections at the British Museum the author has been enabled to clear up many points in synonymy, etc., which have for nearly eighty years remained doubtful and obscure. The most important results of the investigations may be summarised as follows:—One of the beetles has been found by Mr Gahan, of the British Museum, to be the type of a new genus, which is characterised in the present paper, while the specimen upon which it is founded is probably unique; it has been found necessary to rename one species of butterfly and one beetle; errors in synonymy have been corrected in the case of nineteen species; and eight species hitherto wrongly placed have been referred to their proper genera.

Type specimens of beetles (Insecta: Coleoptera) at the museo entomológico Francisco Luís Gallego, Medellín, Colombia

Zootaxa ◽  
2009 ◽  
Vol 2017 (1) ◽  
pp. 65-68
Author(s):  
PAULA A. SEPÚLVEDA-CANO ◽  
MANUEL A. RAMÍREZ-MORA
Keyword(s):  
Natural History ◽  
Liquid Medium ◽  
Species Level ◽  
Zoological Nomenclature ◽  
International Code ◽  
Immature Stages ◽  
Type Specimens ◽  
Northeastern Region ◽  
Natural History Collections ◽  
Almost All

Type specimens are the most scientifically valuable specimens of the natural history collections, and are very important to because they represent standards of reference that provide objectivity in scientific nomenclature (IZCN, 1999). In consideration of the recommendation 72F.4 of the International Code of Zoological Nomenclature, which indicates that the type lists should be published, we provide a list of the species of Coleoptera with types housed in the Museo Entomológico Francisco Luis Gallego (MEFLG). The MEFLG collection originated in 1937 at the Universidad Nacional de Colombia Sede Medellín is the most important insect collection of the northeastern region of Colombia. This museum contains nearly 200,000 specimens of which about 50,000 represent the order Coleoptera, a majority of them are pinned adults and some are immature stages conserved in a liquid medium. The Coleoptera have been identified to subfamily and genus, and some to species level. Almost all of them were collected in Antioquia state, and others are from different localities in Colombia or are donations by foreign institutions.

scholarly journals DINA: Open Source and Open Services - A modern approach for natural history collection management systems and research

2019 ◽  
Vol 3 ◽  
Author(s):  
Falko Glöckler ◽  
James Macklin ◽  
Fredrik Ronquist ◽  
Jana Hoffmann
Keyword(s):  
Natural History ◽  
Open Source ◽  
Management System ◽  
Research Data ◽  
Collection Management ◽  
Modern Approach ◽  
Natural History Collection ◽  
Collection Management System ◽  
Model Complex ◽  
Code Development

The DINA Consortium (“DIgital information system for NAtural history data”, https://dina-project.net ) was formed in order to provide a framework for like-minded large natural history collection-holding institutions to collaborate through a distributed Open Source development model to produce a flexible and sustainable collection management system. Target collections include zoological, botanical, mycological, geological and paleontological collections, living collections, biodiversity inventories, observation records, and molecular data. DINA is funded by the participating member institutions. DINA Core Members are organizations or individuals who commit at least one half-time equivalent of resources to the development of the consortium goals, at least half of which should be available for code development. The DINA system is architected as a loosely-coupled set of several web-based modules. The conceptual basis for this modular ecosystem is a compilation of comprehensive guidelines for Web application programming interfaces (APIs) to guarantee the interoperability of its components. Thus, all DINA components can be modified or even replaced by other components without crashing the rest of the system as long as they are DINA compliant. Furthermore, the modularity enables the institutions to host only the components they need. DINA focuses on an Open Source software philosophy and on community-driven open development, so the contributors share their development resources and expertise outside of their own institutions. One of the overarching reasons to develop a new collection management system is the need to better model complex relationships between collection objects (typically specimens), research data and associated workflows. We will present the enhancements provided by the approach of the DINA system focussing on the flexibility to plug in compliant components and accommodate additional (meta-)data and specimen related research data with the help of a generic data module. Furthermore, we will discuss challenges in the governance of the development activities such as organizing the distributed code development of the core modules, the code review process and the choice of the software stack. These organizational challenges will be overcome with the help of a revised Memorandum of Understanding.

scholarly journals DINA—Development of open source and open services for natural history collections & research

2020 ◽  
Vol 4 ◽  
Author(s):  
Falko Glöckler ◽  
James Macklin ◽  
David Shorthouse ◽  
Christian Bölling ◽  
Satpal Bilkhu ◽  
...  
Keyword(s):  
Natural History ◽  
Open Source ◽  
Open Source Software ◽  
Web Application ◽  
Tracking System ◽  
Molecular Data ◽  
Collection Management ◽  
Agile Development ◽  
Natural History Collections ◽  
Code Base

The DINA Consortium (DINA = “DIgital information system for NAtural history data”, https://dina-project.net) is a framework for like-minded practitioners of natural history collections to collaborate on the development of distributed, open source software that empowers and sustains collections management. Target collections include zoology, botany, mycology, geology, paleontology, and living collections. The DINA software will also permit the compilation of biodiversity inventories and will robustly support both observation and molecular data. The DINA Consortium focuses on an open source software philosophy and on community-driven open development. Contributors share their development resources and expertise for the benefit of all participants. The DINA System is explicitly designed as a loosely coupled set of web-enabled modules. At its core, this modular ecosystem includes strict guidelines for the structure of Web application programming interfaces (APIs), which guarantees the interoperability of all components (https://github.com/DINA-Web). Important to the DINA philosophy is that users (e.g., collection managers, curators) be actively engaged in an agile development process. This ensures that the product is pleasing for everyday use, includes efficient yet flexible workflows, and implements best practices in specimen data capture and management. There are three options for developing a DINA module: create a new module compliant with the specifications (Fig. 1), modify an existing code-base to attain compliance (Fig. 2), or wrap a compliant API around existing code that cannot be or may not be modified (e.g., infeasible, dependencies on other systems, closed code) (Fig. 3). create a new module compliant with the specifications (Fig. 1), modify an existing code-base to attain compliance (Fig. 2), or wrap a compliant API around existing code that cannot be or may not be modified (e.g., infeasible, dependencies on other systems, closed code) (Fig. 3). All three of these scenarios have been applied in the modules recently developed: a module for molecular data (SeqDB), modules for multimedia, documents and agents data and a service module for printing labels and reports: The SeqDB collection management and molecular tracking system (Bilkhu et al. 2017) has evolved through two of these scenarios. Originally, the required architectural changes were going to be added into the codebase, but after some time, the development team recognised that the technical debt inherent in the project wasn’t worth the effort of modification and refactoring. Instead a new codebase was created bringing forward the best parts of the system oriented around the molecular data model for Sanger Sequencing and Next Generation Sequencing (NGS) workflows. In the case of the Multimedia and Document Store module and the Agents module, a brand new codebase was established whose technology choices were aligned with the DINA vision. These two modules have been created from fundamental use cases for collection management and digitization workflows and will continue to evolve as more modules come online and broaden their scope. The DINA Labels & Reporting module is a generic service for transforming data in arbitrary printable layouts based on customizable templates. In order to use the module in combination with data managed in collection management software Specify (http://specifysoftware.org) for printing labels of collection objects, we wrapped the Specify 7 API with a DINA-compliant API layer called the “DINA Specify Broker”. This allows for using the easy-to-use web-based template engine within the DINA Labels & Reports module without changing Specify’s codebase. In our presentation we will explain the DINA development philosophy and will outline benefits for different stakeholders who directly or indirectly use collections data and related research data in their daily workflows. We will also highlight opportunities for joining the DINA Consortium and how to best engage with members of DINA who share their expertise in natural science, biodiversity informatics and geoinformatics.

Sign in / Sign up

Export Citation Format

Share Document