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.

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 Open source web content management systems analysis: the use of server resources

2010 ◽  
Vol 51 ◽  
Author(s):  
Beatričė Andziulienė ◽  
Povilas Narbutas
Keyword(s):  
Management System ◽  
Content Management ◽  
Database Management System ◽  
Management Systems ◽  
Content Management System ◽  
Web Content ◽  
Five Phases ◽  
System Selection ◽  
System Effectiveness ◽  
Content Management Systems

Give general the most appropriate content management system selection stages of the process, divided into five phases. The last stage of the selection proposed by the Web content management system effectiveness analysis. The analysis of Drupal, Joomla!, Xoops content management systems, efficient use of server resources in three cases: the generation of dynamic pages, cache page and cache page with data compression. Content management systems are compared using the following criteria: the maximum number of queries per second, queries pending, RAM usage, CPU load, database management system load. It was found most effective resources of a server using a Web content management system.

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.

MEDIC: An on Site Designed Data Management System for Cardiology

1979 ◽  
Vol 18 (04) ◽  
pp. 199-202 ◽  
Author(s):  
F. Lustman ◽  
P. Lanthier ◽  
D. Charbonneau
Keyword(s):  
Data Management ◽  
Management System ◽  
Selection Process ◽  
Low Cost ◽  
Database Management System ◽  
Data Management System ◽  
Data Quality Control ◽  
Data Definition ◽  
And Performance ◽  
Data Independence

A patient-oriented data management system is described. The environment was cardiology with a heavy emphasis on research and the MEDIC system was designed to meet the day to day program needs. The data are organized in speciality files with dynamic patient records composed of subrecords of different types. The schema is described by a data definition language. Application packages include data quality control, medical reporting and general inquiry.After five years of extensive use in various clinical applications, its utility has been assessed as well as its low cost. The disadvantages, the main being the multifile structure, can now be stated as its advantages, like data independence and performance increase. Although the system is now partially outdated, the experience acquired with its use becomes very helpful in the selection process of the future database management system.

The Reduviidae (Hemiptera: Heteroptera) of Alabama, with a morphological key to species

Zootaxa ◽  
2019 ◽  
Vol 4688 (2) ◽  
pp. 151-198
Author(s):  
C.SCOTT CLEM ◽  
DANIEL R. SWANSON ◽  
CHARLES H. RAY
Keyword(s):  
United States ◽  
Natural History ◽  
The United States ◽  
The State ◽  
Key To Species ◽  
Auburn University ◽  
Natural History Collections ◽  
Assassin Bug ◽  
Morphological Species ◽  
University Museum

Alabama is one of the most speciose states in the United States, yet many common groups of organisms, including assassin bugs (Hemiptera: Heteroptera: Reduviidae), have yet to be fully documented. The purpose of this manuscript is to identify all known assassin bug species occurring in the state using literature records and specimens from natural history collections, most notably the Auburn University Museum of Natural History Entomology Collection, to provide new state records, a checklist, and a morphological species key of the Alabama Reduviidae. All total, 61 species within 36 genera and 10 subfamilies are reported from Alabama. Additionally, 40 new state literature records are documented: 34 from Alabama and six from other states. 

scholarly journals Perancangan Dan Implementasi Private Cloud Storage Dengan Owncloud Pada Jaringan Lokal Menggunakan Virtualbox

2019 ◽  
Vol 1 (2) ◽  
pp. 60-71
Author(s):  
Andi Setiadi Manalu ◽  
Sahat Sonang Sitanggang
Keyword(s):  
Cloud Computing ◽  
Management System ◽  
Database Management ◽  
Cloud Storage ◽  
Web Server ◽  
Content Management ◽  
Database Management System ◽  
Content Management System ◽  
Private Cloud ◽  
Memory Card

Teknologi Cloud Computing dengan layanan Private Cloud Storage merupakan dan menjadi sebuah jawaban untuk permasalahan yang sering terjadi dikehidupan kita sehari-hari yaitu pada permasalahan penggunaan perangkat penyimpanan fisik seperti memory card, flashdisk dan harddisk dimana data-data yang ada didalamnya sering terjadi kerusakan seperti kerusakan fisik perangkat, terkena bad sector, terkena virus, perangkat hilang dan lain sebagainya seperti yang sering terjadi pada mahasiswa dan mahasiswi Politeknik Bisnis Indonesia Murni Sadar Pematangsiantar. Teknologi Cloud Storage yang akan dirancang bersifat private hanya untuk kalangan kampus dan pada jaringan lokal kampus yang tersedia. Perancangan sistem yang akan dilakukan menggunakan virtualisasi dengan Oracle VM VirtualBox. Sistem operasi menggunakan Ubuntu Server 14.04.6 LTS, Web Server menggunakan Apache2, DBMS (Database Management System) menggunakan Mariadb, Interpreter menggunakan PHP dan Content Management System (CMS) menggunakan Owncloud. Setelah perancangan sistem dilakukan kemudian sistem tersebut diimplementasikan pada VirtualBox setelah itu dilakukan pengujian sistem terhadap akses data ke sistem dengan Smartphone dan komputer sehingga didapatkan sebuah sistem yang dapat berjalan dan berfungsi dengan baik agar dapat meningkatkan efisiensi perkuliahan.

scholarly journals Current State of Collections Management Strategies, Standards and Procedures in the Entomology Department at the Durban Natural Science Museum, South Africa

2018 ◽  
Vol 2 ◽  
pp. e26289
Author(s):  
Natasha Govender
Keyword(s):  
South Africa ◽  
Natural Science ◽  
Management System ◽  
Database Management System ◽  
Science Museum ◽  
Training Data ◽  
Management Policy ◽  
Data Management System ◽  
Research Database ◽  
Collections Management

The Durban Natural Science Museum (DNSM) is located in the city of Durban in KwaZulu-Natal province, South Africa. Its entomology collection is one of three main collections at the museum. The collection consists of 141,000 dried specimens and encompasses 25 of the 29 known insect orders. Most of the specimens originate from South Africa however there is also a small percentage which has international origins. Collection growth is perpetuated by field collection trips and donations. In the recent past, DNSM was afforded the opportunity, through the South African National Research Foundation (NRF) via the Natural History Collections (NHC) Funding Instrument, to digitise insect type specimens and move the entomology research database from Microsoft Access to the web-based data management system, Specify 7. These developments have improved accessibility to the collection especially by those who do not have direct contact and access to the collection. In preparation for the migration to Specify 7, the specimen data was cleaned and standardised by means of an open source online tool, OpenRefine. The tool enabled the analysis and correction of data using an automated process which allowed for maximum productivity. Henceforth, we will ensure that the errors encountered during the data cleaning process will not be repeated. This will be achieved by training data capturers on correct formatting standards and using pick lists in the new database management system to foster consistency. On-going collections care is a core component of the DNSM, however a collections management policy is lacking and therefore such procedures differ somewhat across the three core departments. With regards to the entomology department, temperature and humidity monitoring efforts and mould prevention, detection and collection recovery occur regularly. Durban is a coastal city, and the characteristic high humidity is of great concern because it facilitates mould development on the specimens. Regular monitoring procedures mitigate such outbreaks. The DNSM has joined South Africa’s newly launched Natural Science Collections Facility (NSCF) which is a network of institutions which maintain zoological, botanical and paleontological collections. The NSCF, in consultation with institution representatives, has initiated the development of a collections management policy document which will be adopted by the DNSM as one of its sub-policies once it has been passed. The Durban Natural Science Museum will continue to strive for international best practises in collections management.

scholarly journals Assessment of North American arthropod collections: prospects and challenges for addressing biodiversity research

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8086 ◽  
Author(s):  
Neil S. Cobb ◽  
Lawrence F. Gall ◽  
Jennifer M. Zaspel ◽  
Nicolas J. Dowdy ◽  
Lindsie M. McCabe ◽  
...  
Keyword(s):  
United States ◽  
Natural History ◽  
North American ◽  
The United States ◽  
Biodiversity Data ◽  
Biodiversity Crisis ◽  
Biodiversity Research ◽  
Natural History Collections ◽  
Rate Of Increase ◽  
Crucial Information

Over 300 million arthropod specimens are housed in North American natural history collections. These collections represent a “vast hidden treasure trove” of biodiversity −95% of the specimen label data have yet to be transcribed for research, and less than 2% of the specimens have been imaged. Specimen labels contain crucial information to determine species distributions over time and are essential for understanding patterns of ecology and evolution, which will help assess the growing biodiversity crisis driven by global change impacts. Specimen images offer indispensable insight and data for analyses of traits, and ecological and phylogenetic patterns of biodiversity. Here, we review North American arthropod collections using two key metrics, specimen holdings and digitization efforts, to assess the potential for collections to provide needed biodiversity data. We include data from 223 arthropod collections in North America, with an emphasis on the United States. Our specific findings are as follows: (1) The majority of North American natural history collections (88%) and specimens (89%) are located in the United States. Canada has comparable holdings to the United States relative to its estimated biodiversity. Mexico has made the furthest progress in terms of digitization, but its specimen holdings should be increased to reflect the estimated higher Mexican arthropod diversity. The proportion of North American collections that has been digitized, and the number of digital records available per species, are both much lower for arthropods when compared to chordates and plants. (2) The National Science Foundation’s decade-long ADBC program (Advancing Digitization of Biological Collections) has been transformational in promoting arthropod digitization. However, even if this program became permanent, at current rates, by the year 2050 only 38% of the existing arthropod specimens would be digitized, and less than 1% would have associated digital images. (3) The number of specimens in collections has increased by approximately 1% per year over the past 30 years. We propose that this rate of increase is insufficient to provide enough data to address biodiversity research needs, and that arthropod collections should aim to triple their rate of new specimen acquisition. (4) The collections we surveyed in the United States vary broadly in a number of indicators. Collectively, there is depth and breadth, with smaller collections providing regional depth and larger collections providing greater global coverage. (5) Increased coordination across museums is needed for digitization efforts to target taxa for research and conservation goals and address long-term data needs. Two key recommendations emerge: collections should significantly increase both their specimen holdings and their digitization efforts to empower continental and global biodiversity data pipelines, and stimulate downstream research.

scholarly journals Engaging K-12 Audiences with Biodiversity Data through Advancing Digitization for Biodiversity Collections

2018 ◽  
Vol 2 ◽  
pp. e26473
Author(s):  
Molly Phillips ◽  
Anne Basham ◽  
Marc Cubeta ◽  
Kari Harris ◽  
Jonathan Hendricks ◽  
...  
Keyword(s):  
Natural History ◽  
The United States ◽  
Lessons Learned ◽  
Educational Resources ◽  
Digital Data ◽  
Science Standards ◽  
Global Biodiversity Information Facility ◽  
Digital Collections ◽  
Natural History Collections ◽  
K 12

Natural history collections around the world are currently being digitized with the resulting data and associated media now shared online in aggregators such as the Global Biodiversity Information Facility and Integrated Digitized Biocollections (iDigBio). These collections and their resources are accessible and discoverable through online portals to not only researchers and collections professionals, but to educators, students, and other potential downstream users. Primary and secondary education (K-12) in the United States is going through its own revolution with many states adopting Next Generation Science Standards (NGSS https://www.nextgenscience.org/). The new standards emphasize science practices for analyzing and interpreting data and connect to cross-cutting concepts such as cause and effect and patterns. NGSS and natural history collections data portals seem to complement each other. Nevertheless, many educators and students are unaware of the digital resources available or are overwhelmed with working in aggregated databases created by scientists. To better address this challenge, participants within the National Science Foundation Advancing Digitization for Biodiversity Collections program (ADBC) have been working to increase awareness of, and scaffold learning for, digitized collections with K-12 educators and learners. They are accomplishing this through individual programs at institutions across the country as part of the Thematic Collections Networks and collaboratively through the iDigBio Education and Outreach Working Group. ADBC partners have focused on incorporating digital data and resources into K-12 classrooms through training workshops and webinars for both educators and collections professionals, as well as through creating educational resources, websites, and applications that use digital collections data. This presentation includes lessons learned from engaging K-12 audiences with digital data, summarizes available resources for both educators and collections professionals, shares how to become involved, and provides ways to facilitate transfer of educational resources to the K-12 community.

Choosing an Engineering Object Data Management System

1992 ◽  
Author(s):  
Chet Wood
Keyword(s):  
Data Management ◽  
Management System ◽  
Database Management ◽  
Object Oriented ◽  
Database Management System ◽  
Data Management System ◽  
Object Database ◽  
The Right ◽  
Data Requirements ◽  
Object Oriented Database

Abstract An Object Database Management System (ODMS) can be a very useful component when developing applications for use in engineering and manufacturing. Choosing the right product requires a thorough analysis of the data requirements of one’s application, and an equally thorough study of the characteristics of the vendor products. Over a period of about two years, data was gathered on the products of object oriented database manufacturers and researchers. As an example of how to analyze database requirements, an overview of the requirements of our application is presented, followed by a tutorial on the elements and features provided by an ODMS. A brief description is given of each of about a dozen products. Finally, there are tables comparing specific features of a number of these systems.

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