scholarly journals Introduction to the Symposium: Improving access to hidden scientific data in the Biodiversity Heritage Library

2019 ◽  
Vol 3 ◽  
Author(s):  
Constance Rinaldo
Keyword(s):  
Character Recognition ◽  
Optical Character Recognition ◽  
Scientific Data ◽  
Text Search ◽  
Global Biodiversity Information Facility ◽  
The World ◽  
Species Specific ◽  
Program Interface ◽  
Biodiversity Information ◽  
Scientific Name

This will be a short introduction to the symposium: Improving access to hidden scientific data in the Biodiversity Heritage Library. The symposium will present examples of how the Biodiversity Heritage Library (BHL) collaborates across the international consortium and with community partners around the world to help enhance access to the biodiversity literature. Literature repositories, particularly the BHL collections, have been recognized as critical to the global scientific community. A diverse global user community propels BHL and BHL users to develop access tools beyond the standard “title, author, subject” search. BHL utilizes the Global Names Recognition and Discovery (GNRD) service to identify taxonomic names within text rendered by Optical Character Recognition (OCR) software, enabling scientific name searches and creation of species-specific bibliographies, critical to systematics research. In this symposium, we will hear from international partners and creative users making data from the BHL globally accessible for the kinds of larger-scale analysis enabled by BHL’s full-text search capabilities and Application Program Interface (API) protocols. In addition to taxonomic name services already incorporated in BHL, the consortium has also begun exploring georeferencing strategies for better searching and potential connections with key biodiversity resources such as the Global Biodiversity Information Facility (GBIF). With many different institutions around the world participating, the ability to work together virtually is critical for a seamless end product that meets the demands of the international community as well as the needs of local institutions.

scholarly journals ITIS and the Global Taxonomic Backbone

2021 ◽  
Vol 5 ◽  
Author(s):  
David Mitchell ◽  
Thomas Orrell
Keyword(s):  
Scientific Data ◽  
Biological Data ◽  
Global Biodiversity Information Facility ◽  
Global Database ◽  
The Public ◽  
Taxonomic Information ◽  
The World ◽  
Biological Data Management ◽  
Biodiversity Information ◽  
Scientific Name

The Integrated Taxonomic Information System (ITIS) provides a regularly updated, global database that currently contains over 868,000 scientific names and their hierarchy. The program exists to communicate a comprehensive taxonomy of global species across 7 kingdoms that enables biodiversity information to be discovered, indexed, and connected across all human endeavors. ITIS partners with taxonomists and experts across the world to assemble scientific names and their taxonomic relationships, and then distributes that data through publicly available software. A single taxon may be represented by multiple scientific names, so ITIS makes it a priority to provide synonymy. Linking valid or accepted names with their subjective and objective synonyms is a key component of name translation and increases the precision of searches and organization of information. ITIS and its partner Species2000 create the Catalogue of Life (CoL) checklist that provides quality scientific name data for over 2.2M species. The CoL is the Global Biodiversity Information Facility (GBIF) taxonomic backbone. Providing automated open access to complete, current, literature-referenced, and expert-validated taxonomic information enables biological data management systems, and is elemental to enhancing the utility of the amassed scientific data across the world. Fully leveraging this information for the public good is crucial for empowering the global digital society to confront the most pressing social and environmental challenges.

Development and Deployment of an Ethnobotanical and Phytochemical Knowledge Database of Malaysia

2013 ◽  
Vol 64 (2) ◽  
Author(s):  
Shakina Mohd Talkah ◽  
Iylia Zulkiflee ◽  
Mohd Shahir Shamsir
Keyword(s):  
Scientific Literature ◽  
Pharmaceutical Compounds ◽  
South East Asia ◽  
Online Database ◽  
Global Biodiversity Information Facility ◽  
Knowledge Database ◽  
Global Biodiversity ◽  
Digital Knowledge ◽  
Biodiversity Information ◽  
Scientific Name

Currently, all the information regarding ethnobotanical, phytochemical and pharmaceutical information of South East Asia are scattered over many different publications, depositories and databases using various digital and analogue formats. Although there are taxonomic databases of medicinal plants, they are not linked to phytochemical and pharmaceutical information which are often resides in scientific literature. We present Phyknome; an ethnobotanical and phytochemical database with more than 22,000 species of ethnoflora of Asia. The creation of this database will enable a biotechnology researcher to seek and identify ethnobotanical information based on a species’ scientific name, description and phytochemical information. It is constructed using a digitization pipeline that allow high throughput digitization of archival data, an automated dataminer to mine for pharmaceutical compounds information and an online database to integrated these information. The main functions include an automated taxonomy, bibliography and API interface with primary databases such as Global Biodiversity Information Facility (GBIF). We believe that Phyknome will contribute to the digital knowledge ecosystem to elevate access and provide tools for ethnobotanical research and contributes to the management, assessment and stewardship of biodiversity. The database is available at http://mapping.fbb.utm.my/phyknome/.

scholarly journals Contribution to a reference library of DNA barcodes for Colombian freshwater fishes

2021 ◽  
Author(s):  
Manuela Mejía Estrada ◽  
Luz Fernanda Jiménez-Segura ◽  
Iván Soto Calderón
Keyword(s):  
Dna Sequences ◽  
Freshwater Fishes ◽  
Dna Barcodes ◽  
Reference Library ◽  
Global Biodiversity Information Facility ◽  
The World ◽  
Poecilia Sphenops ◽  
Key Indicators ◽  
Biodiversity Information ◽  
Occurrence Records

The Barcoding was proposed motivated by the mismatch between the low number of taxonomists that contrasts with the large number of species, the method requires the construction of reference collections of DNA sequences that represent existing biodiversity. Freshwater fishes are key indicators for understanding biogeography around the world. Colombia with 1610 species of freshwater fishes is the second richest country in the world in this group. However, genetic information of the species continues to be limited, the contribution to a reference library of DNA barcodes for Colombian freshwater fishes highlights the importance of biological collections and seeks to strengthen inventories and taxonomy of such collections in future studies. This dataset contributes to the knowledge on the DNA barcodes and occurrence records of 96 species of Freshwater fishes from Colombia. The species represented in this dataset correspond to an addition to BOLD public databases of 39 species. Forty-nine specimens were collected in Atrato bassin and 708 in Magdalena-Cauca bassin during the period of 2010 to 2020, two species (Loricariichthys brunneus and Poecilia sphenops) are considered exotic to the Atrato, Cauca and Magdalena basins and four species (Oncorhynchu mykiss, Oreochromis niloticus, Parachromis friedrichsthalii and Xiphophorus helleri) are exotic to Colombian hydrogeographic regions. All specimens are deposited in the CIUA collection at University of Antioquia and have their DNA barcodes made publicly available in the Barcode of Life Data System (BOLD) online database and the distribution dataset can be freely accessed through the Global Biodiversity Information Facility (GBIF).

scholarly journals Improving Optical Character Recognition Techniques

2018 ◽  
Vol 7 (2.24) ◽  
pp. 361 ◽  
Author(s):  
Nitin Ramesh ◽  
Aksha Srivastava ◽  
K Deeba
Keyword(s):  
Character Recognition ◽  
Optical Character Recognition ◽  
Document Image ◽  
Text Recognition ◽  
Digital Form ◽  
Written Text ◽  
Optical Character ◽  
Research Organizations ◽  
The World

Document text recognition uses a concept called OCR (optical character recognition),which is the recognition of printed or written text characters by a computer. This involves scanning a document containing text, and converting character by character to their digital form. Thus, it is defined as the process of digitizing a document image into its constituent characters. Equipment used to obtain clearer images for analysis are cameras and flatbed scanners. Even though it’s been out in the world since 1870, the OCR technology is yet to reach perfection. This demanding nature of Optical Character Recognition has made various researchers, industries and technology enthusiasts to divulge their attention to this field. In recent times one can notice a significant increase in the number of research organizations investing their time and effort in this field. In this research, the progress, different aspects and various issues revolving in this field have been summarized. The aim is to present a scrupulous overview of various proposals, advancements and discussions aimed at resolving various problems that arise in traditional OCR.  

Searchable Turkish OCRed historical newspaper collection 1928–1942

2021 ◽  
pp. 016555152110006
Author(s):  
Houssem Menhour ◽  
Hasan Basri Şahin ◽  
Ramazan Nejdet Sarıkaya ◽  
Medine Aktaş ◽  
Rümeysa Sağlam ◽  
...  
Keyword(s):  
Character Recognition ◽  
Optical Character Recognition ◽  
Named Entity Recognition ◽  
Early Modern Period ◽  
Entity Recognition ◽  
Text Search ◽  
Cultural Form ◽  
Named Entity ◽  
Search Mechanism ◽  
Original Website

The newspaper emerged as a distinct cultural form in early 17th-century Europe. It is bound up with the early modern period of history. Historical newspapers are of utmost importance to nations and its people, and researchers from different disciplines rely on these papers to improve our understanding of the past. In pursuit of satisfying this need, Istanbul University Head Office of Library and Documentation provides access to a big database of scanned historical newspapers. To take it another step further and make the documents more accessible, we need to run optical character recognition (OCR) and named entity recognition (NER) tasks on the whole database and index the results to allow for full-text search mechanism. We design and implement a system encompassing the whole pipeline starting from scrapping the dataset from the original website to providing a graphical user interface to run search queries, and it manages to do that successfully. Proposed system provides to search people, culture and security-related keywords and to visualise them.

scholarly journals Algorithms for connecting scientific names with literature in the Biodiversity Heritage Library via the Global Names Project and Catalogue of Life

2021 ◽  
Vol 5 ◽  
Author(s):  
Geoffrey Ower ◽  
Dmitry Mozzherin
Keyword(s):  
Natural History ◽  
Character Recognition ◽  
Optical Character Recognition ◽  
Application Programming Interface ◽  
Species Description ◽  
Biological Research ◽  
Names Project ◽  
Taxonomic Research ◽  
Original Species ◽  
Scientific Name

Being able to quickly find and access original species descriptions is essential for efficiently conducting taxonomic research. Linking scientific name queries to the original species description is challenging and requires taxonomic intelligence because on average there are an estimated three scientific names associated with each currently accepted species, and many historical scientific names have fallen into disuse from being synonymized or forgotten. Additionally, non-standard usage of journal abbreviations can make it difficult to automatically disambiguate bibliographic citations and ascribe them to the correct publication. The largest open access resource for biodiversity literature is the Biodiversity Heritage Library (BHL), which was built by a consortium of natural history institutions and contains over 200,000 digitized volumes of natural history publications spanning hundreds of years of biological research. Catalogue of Life (CoL) is the largest aggregator of scientific names globally, publishing an annual checklist of currently accepted scientific names and their historical synonyms. TaxonWorks is an integrative web-based workbench that facilitates collaboration on biodiversity informatics research between scientists and developers. The Global Names project has been collaborating with BHL, TaxonWorks, and CoL to develop a Global Names Index that links all of these services together by finding scientific names in BHL and using the taxonomic intelligence provided by CoL to conveniently link directly to the page referenced in BHL. The Global Names Index is continuously updated as metadata is improved and digitization technologies advance to provide more accurate optical character recognition (OCR) of scanned texts. We developed an open source tool, “BHLnames,” and launched a restful application programming interface (API) service with a freely available Javascript widget that can be embedded on any website to link scientific names to literature citations in BHL. If no bibliographic citation is provided, the widget will link to the oldest name usage in BHL, which often is the original species description. The BHLnames widget can also be used to browse all mentions of a scientific name and its synonyms in BHL, which could make the tool more broadly useful for studying the natural history of any species.

scholarly journals Using the Taxonomic Backbone(s): The challenge of selecting a taxonomic resource and integrating it with a collection management solution

2021 ◽  
Vol 5 ◽  
Author(s):  
Teresa Mayfield-Meyer ◽  
Phyllis Sharp ◽  
Dusty McDonald
Keyword(s):  
Marine Invertebrate ◽  
Marine Species ◽  
Collection Management ◽  
Global Biodiversity Information Facility ◽  
The World ◽  
Name Matching ◽  
Research Grade ◽  
Global Biodiversity ◽  
Biodiversity Information ◽  
Insight Into

The reality is that there is no single “taxonomic backbone”, there are many: the Global Biodiversity Information Facility (GBIF) Backbone Taxonomy, the World Register of Marine Species (WoRMS) and MolluscaBase, to name a few. We could view each one of these as a vertebra on the taxonomic backbone, but even that isn’t quite correct as some of these are nested within others (MolluscaBase contributes to WoRMS, which contributes to Catalogue of Life, which contributes to the GBIF Backbone Taxonomy). How is a collection manager without expertise in a given set of taxa and a limited amount of time devoted to finding the “most current” taxonomy supposed to maintain research grade identifications when there are so many seemingly authoritative taxonomic resources? And once a resource is chosen, how can they seamlessly use the information in that resource? This presentation will document how the Arctos community’s use of the taxon name matching service Global Names Architecture (GNA) led one volunteer team leader in a marine invertebrate collection to attempt to make use of WoRMS taxonomy and how her persistence brought better identifications and classifications to a community of collections. It will also provide insight into some of the technical and curatorial challenges involved in using an outside resource as well as the ongoing struggle to keep up with changes as they occur in the curated resource.

scholarly journals Harvestmen occurrence database (Arachnida, Opiliones) of the Museu Paraense Emílio Goeldi, Brazil

2019 ◽  
Vol 7 ◽  
Author(s):  
Valéria da Silva ◽  
Manoel Aguiar-Neto ◽  
Dan Teixeira ◽  
Cleverson Santos ◽  
Marcos de Sousa ◽  
...  
Keyword(s):  
Public Consultation ◽  
Biodiversity Data ◽  
Global Biodiversity Information Facility ◽  
The Third ◽  
The World ◽  
Northern Brazil ◽  
Global Biodiversity ◽  
The Government ◽  
Biodiversity Information ◽  
Brazilian Biodiversity

We present a dataset with information from the Opiliones collection of the Museu Paraense Emílio Goeldi, Northern Brazil. This collection currently has 6,400 specimens distributed in 13 families, 30 genera and 32 species and holotypes of four species: Imeri ajuba Coronato-Ribeiro, Pinto-da-Rocha & Rheims, 2013, Phareicranaus patauateua Pinto-da-Rocha & Bonaldo, 2011, Protimesius trocaraincola Pinto-da-Rocha, 1997 and Sickesia tremembe Pinto-da-Rocha & Carvalho, 2009. The material of the collection is exclusive from Brazil, mostly from the Amazon Region. The dataset is now available for public consultation on the Sistema de Informação sobre a Biodiversidade Brasileira (SiBBr) (https://ipt.sibbr.gov.br/goeldi/resource?r=museuparaenseemiliogoeldi-collection-aracnologiaopiliones). SiBBr is the Brazilian Biodiversity Information System, an initiative of the government and the Brazilian node of the Global Biodiversity Information Facility (GBIF), which aims to consolidate and make primary biodiversity data available on a platform (Dias et al. 2017). Harvestmen or Opiliones constitute the third largest arachnid order, with approximately 6,500 described species. Brazil is the holder of the greatest diversity in the world, with more than 1,000 described species, 95% (960 species) of which are endemic to the country. Of these, 32 species were identified and deposited in the collection of the Museu Paraense Emílio Goeldi.

scholarly journals Integrating ABCD and DarwinCore: Toward a better foundation for biodiversity information standards

2019 ◽  
Vol 3 ◽  
Author(s):  
Stanley Blum ◽  
Katharine Barker ◽  
Steven J Baskauf ◽  
Walter G. Berendsohn ◽  
Pier Luigi Buttigieg ◽  
...  
Keyword(s):  
Conceptual Modeling ◽  
Data Representation ◽  
Scientific Data ◽  
Formal Ontology ◽  
Basic Formal Ontology ◽  
Global Biodiversity Information Facility ◽  
Ontology Language ◽  
Occurrence Data ◽  
Knowledge Organization System ◽  
Biodiversity Information

For the last 15 years, Biodiversity Information Standards (TDWG) has recognized two competing standards for organism occurrence data, ABCD (Access to Biological Collections Data; Holetschek et al. 2012) and DarwinCore (Wieczorek et al. 2012). These two representations emerged from contrasting strategies for mobilizing information about organism occurrences (also commonly called species occurrence data). ABCD was capable of representing details of more kinds of information, but was necessarily more complicated. DarwinCore, on the other hand, was simpler but more limited in its ability to represent data of different kinds and formats. TDWG endorsed both standards because the different projects and communities that generated them remained dedicated to their different strategies and tool sets, and the Global Biodiversity Information Facility (GBIF) developed the ability to integrate data published in either standard. Since their inceptions, DarwinCore and ABCD have become more similar. DarwinCore has gotten more complicated through the addition of terms and has begun to assign terms to classes. ABCD is now expressed in RDF (Resource Description Framework), potentially enabling re-use of terms with alternative structures among classes. At the same time, methodologies for conceptual modeling and representing complex scientific data have continued to evolve. In particular, a suite of modeling and data representation methods related to linked data and the semantic web, i.e., RDF, SKOS (Simple Knowledge Organization System), and OWL (web Ontology Language), promise to make it easier for us to reconcile shared concepts among different representations or schemas. A mapping between ABCD 2.1 and DarwinCore has existed since before 2005.*1 ABCD 3.0 and DarwinCore are both now represented in RDF. In addition, the BioCollections Ontology (BCO) covers many of the shared concepts and is derived from the Basic Formal Ontology (BFO), an upper level ontology that has oriented many other biomedical ontologies. Reconciling ABCD and DarwinCore through alignment with BCO (in the OBO Foundry; Smith et al. 2007) would better connect TDWG standards to other domains in biology. We appreciate that many working scientists and data managers perceive ontologies as overly complicated. To mitigate the steep learning curve associated with ontologies, we expect to create simpler application profiles or schemas to guide and serve narrower communities of practice within the wider biodiversity domain. We also plan to integrate the current work of the Taxonomic Names and Concepts Interest Group and thereby eliminate the redundancy between DarwinCore and Taxonomic Concepts Transfer Schema (TCS; Kennedy et al. 2006). At the time of this writing, we have only agreements from the authors (i.e., conveners of relevant TDWG Interest Groups and other key stakeholders) to collaborate in pursuit of these common goals. In this presentation we will give a more detailed description of our objectives and products, the methods we are using to achieve them, and our progress to date.

Possible Approaches for Character Recognition With Existing Methodologies and State-of-the-Art Techniques

2019 ◽  
pp. 232-246
Author(s):  
Rashmi Welekar ◽  
Nileshsingh V. Thakur
Keyword(s):  
Character Recognition ◽  
Optical Character Recognition ◽  
State Of The Art ◽  
Industrial Applications ◽  
New Methods ◽  
Optical Character ◽  
The World ◽  
New Hypothesis ◽  
Key Questions ◽  
Art Techniques

The world started to talk about optical character recognition (OCR) around 1870. Then over another 25 years OCR systems were designed for industrial applications. And now the OCR software is easily available online for free, through products like Acrobat reader, WebOCR, etc. But still the research is on. Do we need to switch direction or introduce new hypothesis are some of the key questions? The purpose of this chapter is to answer the above questions and propose new methods for character recognition.

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