# bib

id: jbi-3989
author: Berendsohn, Walter G.; Chavan, Vishwas; Macklin, James
date: 2010
pages: 5
extension: .pdf
mime: application/pdf
words: 2279
sentence: 120
flesch: 34
cache: cache/jbi-3989.pdf
txt: txt/jbi-3989.txt
title:
  Summary of Recommendations of the GBIF Task Group on the Global Strategy and Action Plan for the Digitisation of Natural History Collections

summary:
  Approaches to estimating the universe of natural history collection data. 3: GBIF must continue to improve and promote the global infrastructure used to mobilize digitized collection data 3.1.


id: jbi-1631
author: Güntsch, Anton; Hoffmann, Niels; Kelbert, Patricia; Berendsohn, Walter G.
date: 2009
pages: 6
extension: .pdf
mime: application/pdf
words: 2513
sentence: 151
flesch: 50
cache: cache/jbi-1631.pdf
txt: txt/jbi-1631.txt
title:
  EFFECTIVELY SEARCHING SPECIMEN AND OBSERVATION DATA WITH TOQE, THE THESAURUS OPTIMIZED QUERY EXPANDER

summary:
  53-58 58 as well as Euro+Med plantbase and ERMS, have been added as thesaurus databases. The TOQE query functions are directly integrated into the specimen search interface so that taxonomists can easily pick from the list of available thesaurus systems.


id: jbi-3994
author: Scoble, Malcolm
title: Rationale and Value of Natural History Collections Digitisation
date: 2010
pages: 4
extension: .pdf
mime: application/pdf
words: 2391
sentence: 110
flesch: 41
cache: cache/jbi-3994.pdf
txt: txt/jbi-3994.txt
summary:
  A compelling case for the use of natural history collection data in modeling, alone or, particularly, combined with other types of data, was made by Graham et al. (2004). Approaches to estimating the universe of natural history collections data.


id: jbi-3990
author: Chavan, Vishwas; BERENTS, PENNY; HAMER, MICHELLE
date: 2010
pages: 7
extension: .pdf
mime: application/pdf
words: 3580
sentence: 208
flesch: 37
cache: cache/jbi-3990.pdf
txt: txt/jbi-3990.txt
title:
  TOWARDS DEMAND DRIVEN PUBLISHING: APPROCHES TO THE PRIORITISATION OF DIGITISATION OF NATURAL HISTORY COLLECTIONS DATA

summary:
  We strongly advocate that the collection management and curatorial community develop an institutional or collection specific demand-driven prioritization plan for collection digitization on the basis of content needs of the major stakeholders and the user community. We further recommend that GBIF works with major natural history collection stakeholder communities to develop best practice guidelines for developing (a) institution or collection specific, demand-driven plans for collection digitization, and (b) national or thematic collection digitization strategy and action plans.


id: jbi-1634
author: Jiménez-Valverde, Alberto; Nakazawa, Yoshinori; Lira-Noriega, Andrés; Peterson, A. Townsend
title: ENVIRONMENTAL CORRELATION STRUCTURE AND ECOLOGICAL NICHE MODEL PROJECTIONS
date: 2009
pages: 8
extension: .pdf
mime: application/pdf
words: 3521
sentence: 152
flesch: 45
cache: cache/jbi-1634.pdf
txt: txt/jbi-1634.txt
summary:
  Transferability of species distribution models: A functional habitat approach for two regionally threatened butterflies. Such transferability applications, however, depend critically on the assumption that environmental variables relevant on one landscape or at one time will be relevant on another.


id: jbi-16
author: Chavan, Vishwas Shravan; Rane, Nilesh Sunil; Watve, Aparna; Ruggiero, Michael
title: Resolving taxonmic discrepancies: Role of Electronic Catalogues of Known Organisms
date: 2005
pages: 9
extension: .pdf
mime: application/pdf
words: 4614
sentence: 298
flesch: 47
cache: cache/jbi-16.pdf
txt: txt/jbi-16.txt
summary:
  Hence, to build up easy communication pathways and reduce the time input, it would be extremely helpful to have a web-based central registry system for taxonomic names. In addition, a permanent mechanism for registering and validating scientific names of organisms needs to be created at national as well as global levels.


id: jbi-6
author: Silva, Marcos R.
title: Bioinformatics, the Clearing-House Mechanism and the Convention on Biological Diversity
date: 2004
pages: 7
extension: .pdf
mime: application/pdf
words: 4406
sentence: 188
flesch: 33
cache: cache/jbi-6.pdf
txt: txt/jbi-6.txt
summary:
  Actions to achieve this would include: a) disseminating information in appropriate formats for potential users; b) using best-practice in information management and dissemination; c) supporting the development and implementation of tools, standards and protocols for data exchange that allow more effective sharing of information; d) establishing inter-operable electronic databases that allow for more effective integration of information from multiple sources in real time; e) improving use of the Internet as a tool for access and dissemination of biodiversity data, including increasing access to the Internet; SILVA – THE BIODIVERSITY CONVENTION AND BIOINFORMATICS 26 f) reviewing the adequacy of the existing data, assessing gaps and the action that needs to be taken to fill them.” These goals include facilitating development and implementation of approaches, technologies, and best practices necessary to access, share, and disseminate biodiversity data at the species, ecosystem, and genetic levels via the Internet.


id: jbi-7
author: Stein, Barbara R; Wieczorek, John R.
title: Mammals of the World: MaNIS as an example of data integration in a distributed network environment
date: 2004
pages: 9
extension: .pdf
mime: application/pdf
words: 5648
sentence: 245
flesch: 35
cache: cache/jbi-7.pdf
txt: txt/jbi-7.txt
summary:
  This gazetteer was created by combining locality data from all participating institutions at the outset of the project into a single gazetteer database with an online query interface for browsing and downloading tab-delimited locality records16. This will mean that new specimens added to their collections will have locality data of quality comparable to that which has been achieved in the georeferencing for the MaNIS project.


id: jbi-1633
author: Ch'ng, Eugene
title: AN EFFICIENT SEGMENTATION ALGORITHM FOR ENTITY INTERACTION
date: 2009
pages: 13
extension: .pdf
mime: application/pdf
words: 5973
sentence: 381
flesch: 52
cache: cache/jbi-1633.pdf
txt: txt/jbi-1633.txt
summary:
  Other methods are developed for representing complex outdoor scenes in computer graphics (Snyder and Barr 1987, Deussen et al. 1998, Soler et al. 2003) but algorithms have not been formalised for improving the efficiency of large entity interactions. In theory, the simulation time should decrease with the increase of landscape segments.


id: jbi-19
author: Guralnick, Robert P; Neufeld, David
date: 2005
pages: 14
extension: .pdf
mime: application/pdf
words: 6509
sentence: 359
flesch: 45
cache: cache/jbi-19.pdf
txt: txt/jbi-19.txt
title:
  Challenges Building Online GIS Services to Support Global Biodiversity Mapping and Analysis: Lessons from the Mountain and Plains Database and Informatics project.

summary:
  A key component to sharing and eventually mapping biodiversity data is development of agreed upon standards (Figure 1 – community data standards) for accessing widely varying database structures, and associated metadata (Bowker, 2000). The project, which currently covers a 6-state region (Colorado, Montana, Nebraska, North Dakota, South Dakota, and Wyoming) in the United States, provides users with access to biodiversity data collected over the last 150 yr.


id: jbi-9
author: Sánchez-Cordero, Víctor; Cirelli, Verónica; Munguial, Mariana; Sarkar, Sahotra
title: Place prioritization for biodiversity content using species ecological niche modeling
date: 2005
pages: 13
extension: .pdf
mime: application/pdf
words: 6218
sentence: 366
flesch: 39
cache: cache/jbi-9.pdf
txt: txt/jbi-9.txt
summary:
  Recent studies proposing networks of conservation areas for improving biodiversity conservation include plants and birds in Norway (Saetersdal et al. 1993), plants (Willis et al. 1996), and birds (Godown and Peterson 2000; Fairbanks et al. 2001) in South Africa and the United States, and terrestrial vertebrates in the United States (Csuti et al. 1997). To illustrate these points, we (1) predict distributions under current and future deforestation scenarios for the Mexican endemic mammal Dipodomys phillipsii, and show how areas for restoration may be selected; and (2) propose conservation areas by combining nonvolant mammal distributional predictions as biodiversity surrogates with place prioritization procedures, to connect decreed natural protected areas in a region holding exceptional biodiversity: the Transvolcanic Belt in central Mexico.


id: jbi-3991
author: Ariño, Arturo H.
title: Approaches to estimating the universe of natural history collections data
date: 2010
pages: 12
extension: .pdf
mime: application/pdf
words: 5799
sentence: 249
flesch: 46
cache: cache/jbi-3991.pdf
txt: txt/jbi-3991.txt
summary:
  1: Plot of log of number of specimens from BCI collections against their rank when ordered by size. Distribution data Only 58.6% of BCI collections declare holdings.


id: jbi-17
author: Koning, Drew; Sarkar, Indra Neil; Moritz, Thomas
title: TaxonGrab: Extracting Taxonomic Names From Text
date: 2005
pages: 4
extension: .pdf
mime: application/pdf
words: 2766
sentence: 155
flesch: 45
cache: cache/jbi-17.pdf
txt: txt/jbi-17.txt
summary:
  Since taxonomic names are most typically – though not exclusively – derived from Greek or Latin, filters can be used to separate taxonomic name candidates using a language-specific lexicon (e.g., a lexicon of English words). Because organism nomenclature conforms closely to prescribed rules, automated techniques may be useful for identifying organism names from existing documents, and may also support the completion of comprehensive indices of taxonomic names; such comprehensive lists are not yet available.


id: jbi-1574
author: Downey, Laura; Pennington, Deana
title: BRIDGING THE GAP BETWEEN TECHNOLOGY AND SCIENCE WITH EXAMPLES FROM ECOLOGY AND BIODIVERSITY
date: 2009
pages: 10
extension: .pdf
mime: application/pdf
words: 5752
sentence: 310
flesch: 44
cache: cache/jbi-1574.pdf
txt: txt/jbi-1574.txt
summary:
  They can be categorized into two broad areas: user interface design issues and annotation issues. Table 2 gives a small sample of the kinds of user profile data we collected on SEEK.


id: jbi-36
author: Sautter, Guido; Böhm, Klemens; Agosti, Donat
title: A Quantitative Comparison of XML Schemas for Taxonomic Publications
date: 2007
pages: 13
extension: .pdf
mime: application/pdf
words: 8090
sentence: 424
flesch: 50
cache: cache/jbi-36.pdf
txt: txt/jbi-36.txt
summary:
  Consequently, we expect this extension to affect the performance of Name Queries and Location Queries a little more than the aspect markup. Name Queries and Location Queries execute slower than with the plain aspect markup and with the morphologic index.


id: jbi-3987
author: Baird, Roger Charles
title: Leveraging the fullest potential of scientific collections through digitisation.
date: 2010
pages: 7
extension: .pdf
mime: application/pdf
words: 3846
sentence: 142
flesch: 17
cache: cache/jbi-3987.pdf
txt: txt/jbi-3987.txt
summary:
  Scientific collections can be characterized as assemblages of natural history specimens as well as human history artifacts that have been sufficiently documented, at the time of acquisition or through the course of analysis, as to have lasting value as part of a broad research infrastructure. HOW ARE SCIENTIFIC COLLECTIONS AND THEIR DATA USED?


id: jbi-3314
author: Fernandez, Miguel; Blum, Stanley; Reichle, Steffen; Guo, Qinghua; Holzman, Barbara; Hamilton, Healy
date: 2009
pages: 17
extension: .pdf
mime: application/pdf
words: 9000
sentence: 595
flesch: 50
cache: cache/jbi-3314.pdf
txt: txt/jbi-3314.txt
title:
  LOCALITY UNCERTAINTY AND THE DIFFERENTIAL PERFORMANCE OF FOUR COMMON NICHE-BASED MODELING TECHNIQUES

summary:
  While few studies have measured the sensitivity of distribution models to grid cell size in the environmental layers (Guisan et al. 2007), others have addressed the effect of remote sensing derived products as alternative environmental layers in ENM (Parra et al. 2004; Roura-Pascual et al. 2004; Peterson et al. 2006; Zimmermann et al. 2007; Bradley and Fleishman 2008; Buermann et al. 2008). The influence of spatial errors in species occurrence data used in distribution models.


id: jbi-40
author: Lobo, Jorge M
title: More complex distribution models or more representative data?
date: 2008
pages: 6
extension: .pdf
mime: application/pdf
words: 2847
sentence: 188
flesch: 50
cache: cache/jbi-40.pdf
txt: txt/jbi-40.txt
summary:
  e-mail: mcnj117@mncn.csic.es Abstract.⎯ Distribution models for species are increasingly used to summarize species’ geography in conservation analyses. The influence of random selection of absences on distribution models was illustrated for a large Iberian dung beetle species (Copris hispanus) that occurs mainly in the southern half of the Iberian Peninsula.


id: jbi-39
author: Teeffelen, Astrid van; Moilanen, Atte
title: Where and how to manage: Optimal selection of conservation actions for multiple species.
date: 2008
pages: 13
extension: .pdf
mime: application/pdf
words: 8255
sentence: 474
flesch: 52
cache: cache/jbi-39.pdf
txt: txt/jbi-39.txt
summary:
  1-13 1 WHERE AND HOW TO MANAGE: OPTIMAL SELECTION OF CONSERVATION ACTIONS FOR MULTIPLE SPECIES ASTRID The average value of all possible solutions, Fmean(X), corresponds to the mean expected value when conservation actions are randomly assigned to locations, under the budget constraint.


id: jbi-5
author: Chapman, Arthur D; Muñoz, Mauro E.S.; Koch, Ingrid
date: 2005
pages: 18
extension: .pdf
mime: application/pdf
words: 12354
sentence: 777
flesch: 52
cache: cache/jbi-5.pdf
txt: txt/jbi-5.txt
title:
  Environmental Information: Placing Biodiversity Phenomena in an Ecological and Environmental Context

summary:
  Often these transition zones are not very well delineated in environmental data layers, particularly if the scale is coarse. CONCLUSION Selection of environmental data layers is among the most important aspects of ecological niche modeling.


id: jbi-4
author: Soberon, Jorge; Peterson, A. Townsend
title: Interpretation of Models of Fundamental Ecological Niches and Species' Distributional Areas
date: 2005
pages: 10
extension: .pdf
mime: application/pdf
words: 5121
sentence: 251
flesch: 49
cache: cache/jbi-4.pdf
txt: txt/jbi-4.txt
summary:
  Whereas a mechanistic approach explicitly does not consider B, a correlative approach runs the risk of being biased by such interaction effects—still, it has the potential to take them into account explicitly via inclusion of the geography of other species in single-species models. Once such tools are developed, testing ecological niche models in ecological space will constitute an important step forward in improving the formal nature of ecological niche modeling.


id: jbi-4125
author: Otegui, Javier; Ariño, Arturo H.; Chavan, Vishwas; Gaiji, Samy
title: On the dates of GBIF mobilised primary biodiversity records
date: 2013
pages: 12
extension: .pdf
mime: application/pdf
words: 5993
sentence: 276
flesch: 58
cache: cache/jbi-4125.pdf
txt: txt/jbi-4125.txt
summary:
  Joining data records published by the data publishers into this single data model entails a large amount of data mapping, checking, marking and manipulation. Figure 6 shows a plot of data records in the November 2010 version of the index for occurrences in the XX and XXI century.


id: jbi-3988
author: Berendsohn, Walter G.; Seltmann, Peggy
title: Using geographical and taxonomic metadata to set priorities in specimen digitization
date: 2010
pages: 10
extension: .pdf
mime: application/pdf
words: 5487
sentence: 286
flesch: 40
cache: cache/jbi-3988.pdf
txt: txt/jbi-3988.txt
summary:
  In combination with observation and ecological data, collection data serve to identify global priority areas for conservation action based on taxonomic diversity (Vane-Wright et al. 1991; This is one of the key impediments to effective use of collection information outside the taxonomic community.


id: jbi-4095
author: Endresen, Dag Terje Filip; Knüpffer, Helmut
title: The Darwin Core extension for genebanks opens up new opportunities for sharing genebank datasets
date: 2012
pages: 18
extension: .pdf
mime: application/pdf
words: 11760
sentence: 708
flesch: 49
cache: cache/jbi-4095.pdf
txt: txt/jbi-4095.txt
summary:
  Efficient  Access  to  Distributed  Germplasm  Data   Sets  Stimulates  Novel  Uses   Research integrating genebank passport data (georeferenced occurrence data for the original collecting site) with phenotypic measurements (characterization and evaluation data) and with eco- climatic layers has opened new possibilities for a rational utilization of genebank materials (Bhullar et al., 2009; Endresen, 2010; Endresen et al., 2011; Bari et al., 2011; Endresen et al., 2012b) using the Focused Identification of Germplasm Strategy (FIGS) approach (Mackay and Street, 2004). The new Darwin Core extension for genebanks is required to enable the GBIF IPT to share a standard set of minimum terms for germplasm data sets.


id: jbi-4019
author: King, Nicholas; Krishtalka, Leonard; Chavan, Vishwas
date: 2010
pages: 5
extension: .pdf
mime: application/pdf
words: 2939
sentence: 216
flesch: 31
cache: cache/jbi-4019.pdf
txt: txt/jbi-4019.txt
title:
  Thoughts on implementation of the recommendations of the GBIF Task Group on a Global Strategy and Action Plan for Mobilisation of Natural History Collections Data

summary:
  Dr. Vishwas Chavan is the Senior Programme Officer for DIGIT (Digitization and Mobilization of Primary Biodiversity Data including natural history collections data). Digitization and mobilization of natural history collections data has been an integral part of the Work Programme of the Global Biodiversity Information Facility (GBIF) since its inception in 2001 (OECD, 1999 and GBIF, 2002).


id: jbi-3
author: Canhos, Vanderlei Perez; Souza, Sidnei de; Giovanni, Renato De; Canhos, Dora Ann Lange
title: Global Biodiversity Informatics: setting the scene for a "new world" of ecological forecasting
date: 2004
pages: 13
extension: .pdf
mime: application/pdf
words: 8838
sentence: 512
flesch: 36
cache: cache/jbi-3.pdf
txt: txt/jbi-3.txt
summary:
  Although GBIF intends eventually to incorporate all levels of biodiversity data (molecules to ecosystems), its initial phase is focusing on species- and specimen-level information. Working with its partners, GBIF is promoting development and adoption of standards and protocols for documenting and exchanging biodiversity data.


id: jbi-37
author: Papes, Monica
date: 2007
pages: 13
extension: .pdf
mime: application/pdf
words: 6609
sentence: 370
flesch: 49
cache: cache/jbi-37.pdf
txt: txt/jbi-37.txt
title:
  Ecological Niche Modeling Approaches to Conservation of Endangered and Threatened Birds in Central and Eastern Europe

summary:
  Because existing climate change data sets do not include all of the climatic parameters used in the analyses described above for predicting present species distributions, a second round of GARP models was run for predicting future (post-climate change) potential distributions, based only on annual mean minimum temperature, annual mean temperature, annual mean maximum temperature, annual mean precipitation, topographic index, slope, and aspect. To summarize CEE threatened and endangered bird species’ distributions, I used tools from the field of ecological niche modeling (ENM), and produced predictive models of species’ distributions based on known occurrences of species and raster GIS databases summarizing relevant environmental parameters across the CEE landscape.


id: jbi-3986
author: Foley, Desmond
title: A SPREADSHEET MAPPING APPROACH FOR ERROR CHECKING AND SHARING COLLECTION POINT DATA
date: 2010
pages: 6
extension: .pdf
mime: application/pdf
words: 2719
sentence: 113
flesch: 45
cache: cache/jbi-3986.pdf
txt: txt/jbi-3986.txt
summary:
  In the following I describe a method and provide examples for obtaining Excel chart maps from a shapefile, and from online maps. The use of country and global Excel chart maps allow the detection of some but not all of these possible georeference errors.


id: jbi-3992
author: Vollmar, Ana; Macklin, James Alexander; Ford, Linda
title: Natural History Specimen Digitization: Challenges and Concerns
date: 2010
pages: 20
extension: .pdf
mime: application/pdf
words: 11229
sentence: 478
flesch: 37
cache: cache/jbi-3992.pdf
txt: txt/jbi-3992.txt
summary:
  It discusses issues associated with having collections data available on-line, including how various collections have addressed the difficulty of ensuring feedback about their on-line data. While increasing remote access and on-line use of collections clearly has many benefits, at the same time, it presents difficulties in ensuring that feedback about collections is received, in particular that the work researchers do with collections data on-line make it back to the collection itself.


id: jbi-29
author: Peterson, A. Townsend
title: Uses and Requirements of Ecological Niche Models and Related Distributional Models
date: 2006
pages: 14
extension: .pdf
mime: application/pdf
words: 9604
sentence: 584
flesch: 53
cache: cache/jbi-29.pdf
txt: txt/jbi-29.txt
summary:
  Equilibrium of species' distributions with climate. Building statistical models to analyze species distributions.


id: jbi-3927
author: Franz, Nico M
title: BIOLOGICAL TAXONOMY AND ONTOLOGY DEVELOPMENT: SCOPE AND LIMITATIONS
date: 2011
pages: 22
extension: .pdf
mime: application/pdf
words: 15347
sentence: 984
flesch: 59
cache: cache/jbi-3927.pdf
txt: txt/jbi-3927.txt
summary:
  Vogt et al., 2009; Balhoff et al., 2010; Dahdul et al., 2010; Mungall et al., 2010), and taxonomy (Schulz et al., 2008). This is unfortunate because a thoroughgoing ontology for biological taxonomy could play the same overarching role in the bio- ontological domain that taxonomy plays in biology (Schulz et al., 2008).


id: jbi-25
author: Page, Roderic D. M.
title: Taxonomic names, metadata, and the Semantic Web
date: 2006
pages: 15
extension: .pdf
mime: application/pdf
words: 8195
sentence: 418
flesch: 58
cache: cache/jbi-25.pdf
txt: txt/jbi-25.txt
summary:
  However, I suggest that in the context of taxonomic names, the most compelling benefit of adopting these identifiers comes from the metadata associated with each LSID. –– Life Science Identifiers, metadata, taxonomic names, Semantic Web, RDF, triple stores.


id: jbi-35
author: Neale, Sophie; Pullan, M. R.; Watson, M. F.
title: Online Biodiversity Resources - Principles for Usability
date: 2007
pages: 10
extension: .pdf
mime: application/pdf
words: 6756
sentence: 358
flesch: 54
cache: cache/jbi-35.pdf
txt: txt/jbi-35.txt
summary:
  However in order to more fully develop our arguments we have studied the available documentation from a wide range of biodiversity portal projects (AlgaeBase, BioCASE, BioCISE, CABI Species Fungorum, EMBL reptile database, ENHSIN, ENBI, ERMS, ETI-WBD, ETI-WTD, Fauna Europaea, FishBase, GBIF, SpeciesBank, ILDIS, LINNE, NatureServe, Natuurloket, NBN, Species 2000 Europa and WADSIS). We have also been able to garner considerable information from two recent reports on user requirements analysis in biodiversity portal projects in which the design processes for a wide range of projects were obtained directly from the portal developers (Neale et al. 2005, Schalk and Heitmans 2005).


id: jbi-1626
title: DARWIN CORE BASED DATA STREAMLINING WITH DigiMus 2.0
date: 2009
pages: 4
extension: .pdf
mime: application/pdf
words: 1980
sentence: 129
flesch: 54
cache: cache/jbi-1626.pdf
txt: txt/jbi-1626.txt
author:
  Kakodkar, Aditya P; Kerkar, Sarika S.; Varghese, Neena S.; Kavlekar, Devanand P.; Achuthankutty, C. T.

summary:
  Funding for biological data management in developing countries is much less or entirely nonexistent (Thomson, 2005). In this paper we present a web based open source software tool named “DigiMus 2.0” which enables individuals to manage biological specimen data from their collection and effectively structure it according to Darwin Core data standards v 1.2 ( DwC v 1.2).


id: jbi-4853
title: OMWS: A Web Service Interface for Ecological Niche Modelling
date: 2015
pages: 10
extension: .pdf
mime: application/pdf
words: 5472
sentence: 307
flesch: 48
cache: cache/jbi-4853.pdf
txt: txt/jbi-4853.txt
author:
  Giovanni, Renato De; Torres, Erik; Amaral, Rafael Burlamaqui; Blanquer, Ignacio; Rebello, Vinod; Canhos, Vanderlei Perez

summary:
  Web services are web-based applications that support dynamic interactions with other software applications using open standards that include data formats like eXtensible Markup Language (XML) (World Wide Web Consortium, 2006) to transmit data over a network via Internet- based protocols. Web services provide a standard means of interoperating between different software applications running on a variety of platforms and/or frameworks (World Wide Web Consortium, 2004a).


id: jbi-3631
author: Nilsson-Örtman, Viktor; Nilsson, Anders N.
date: 2010
pages: 16
extension: .pdf
mime: application/pdf
words: 9426
sentence: 643
flesch: 53
cache: cache/jbi-3631.pdf
txt: txt/jbi-3631.txt
title:
  USING TAXONOMIC REVISION DATA TO ESTIMATE THE GLOBAL SPECIES RICHNESS AND CHARACTERISTICS OF UNDESCRIBED SPECIES OF DIVING BEETLES (COLEOPTERA: DYTISCIDAE)

summary:
  Revision of the Nearctic Liodessus affinis (Say 1823) species group (Coleoptera: Dytiscidae, Hydroporinae, Bidessini). To be able to use species description data for this purpose, we must have considered that: 1) the effort spent on taxonomic discovery and description varies greatly over time and between regions; 2) curves showing the rate of description plotted against time often displays a distinct ―lag phase‖ of low description rates in the initial stage; 3) the precise relationship between taxonomic effort and description rate is poorly understood, making it difficult to justify which model to fit to the data; 4) the description process frequently proceed in pronounced leaps marking the publication of important monographic works and revision which are impossible to predict using extrapolation techniques; 5) if there is no sign of decrease in the rate of description over NILSSON-ÖRTMAN & NILSSON - USING TAXONOMIC REVISION DATA TO ESTIMATE SPECIES RICHNESS 7 time, extrapolating techniques cannot be applied (White 1979).


id: jbi-46
author: cui, hong
title: Converting Taxonomic Descriptions to New Digital Formats
date: 2008
pages: 21
extension: .pdf
mime: application/pdf
words: 12323
sentence: 558
flesch: 59
cache: cache/jbi-46.pdf
txt: txt/jbi-46.txt
summary:
  Biodiversity and other factors contribute to the rather skewed distributions of elements in description collections (see the appendix). In description collections, due to the diversities in living organisms, authorship, and editorial policies, the coverage of different organs are quite uneven, resulting in a very skewed distribution of training data for individual elements: for example, in the 310 FNA training examples, there were more than two hundred examples for “leaf blade” but zero for “tendril”.


id: jbi-4117
date: 2013
pages: 13
extension: .pdf
mime: application/pdf
words: 6720
sentence: 314
flesch: 35
cache: cache/jbi-4117.pdf
txt: txt/jbi-4117.txt
author:
  Morris, Robert A; Barve, Vijay; Carausu, Mihail; Chavan, Vishwas; Cuadra, José; Freeland, Chris; Hagedorn, Gregor; Leary, Patrick; Mozzherin, Dimitry; Olson, Annette; Riccardi, Gregory; Teage, Ivan; Whitbread, Greg

title:
  Discovery and publishing of primary biodiversity data associated with multimedia resources: The Audubon Core strategies and approaches

summary:
  Unlike observation or specimen data, however, the network loads and Figure 1: Relationships of multimedia resources to primary types of biodiversity resources, including some well-known example systems. The documentation supporting the submission to TDWG for ratification includes a normative specification of the Audubon Core as a set of multimedia resource metadata terms independent of any digital representation (http://terms.gbif.org/wiki/Audubon_Core_Term_ List_(1.0_normative) ).


id: jbi-4748
date: 2014
pages: 12
extension: .pdf
mime: application/pdf
words: 6167
sentence: 364
flesch: 52
cache: cache/jbi-4748.pdf
txt: txt/jbi-4748.txt
author:
  Mononen, Tero; Tegelberg, Riitta; Sääskilahti, Mira; Huttunen, Markku A.; Tähtinen, Marko; Saarenmaa, Hannu

title:
  DigiWeb - a workflow environment for quality assurance of transcription in digitization of natural history collections

summary:
  When using a well-established imaging method for specimens, scientific expertise is particularly important for transcribing specimen data. Keywords – data entry, mass digitization INTRODUCTION Collections conserved by natural history museums are an important source of information on taxonomy, biodiversity and environmental change.


id: jbi-5007
title: THE PRESENT STATE OF BOTANICAL INVESTIGATIONS IN CÔTE D’IVOIRE
date: 2015
pages: 9
extension: .pdf
mime: application/pdf
words: 4896
sentence: 350
flesch: 66
cache: cache/jbi-5007.pdf
txt: txt/jbi-5007.txt
author:
  KOFFI, Kouao Jean; KOUASSI, Akossoua Faustine; ADOU YAO, Constant Yves; BAKAYOKO, Adama; IPOU, Ipou Joseph; BOGAERT, Jan

summary:
  Le climat de la Côte d’Ivoire. Microsoft Word - Koffi_proofs.docx Biodiversity Informatics, 10, 2015, 56-64   56   THE PRESENT STATE OF BOTANICAL KNOWLEDGE IN CÔTE D’IVOIRE KOUAO JEAN KOFFI1*, AKOSSOUA FAUSTINE KOUASSI2, CONSTANT YVES ADOU YAO3, ADAMA BAKAYOKO1, IPOU JOSEPH IPOU2, JAN BOGAERT4 1University Nangui Abrogoua, UFR-SN, 02 B. P. 801 Abidjan 02, Côte d’Ivoire.


id: jbi-7600
author: Cobos, Marlon E; Jiménez, Laura; Nuñez-Penichet, Claudia; Romero-Alvarez, Daniel; Simoes, Marianna
title: Sample data and training modules for cleaning biodiversity information
date: 2018
pages: 2
extension: .pdf
mime: application/pdf
words: 1039
sentence: 70
flesch: 56
cache: cache/jbi-7600.pdf
txt: txt/jbi-7600.txt
summary:
  Key words: accuracy, data cleaning, error, redundancy, precision, primary biodiversity data The availability and management of large on- line biodiversity databases has become an exciting, although challenging, step in the development of an authoritative and comprehensive basis for biodiver- sity knowledge. Primary biodiversity data have become much more accessible in recent decades, with a major tran- sition from recalcitrance (Graves 2000) to enthusi- asm.


id: jbi-8
author: Martinez-Meyer, Enrique
date: 2005
pages: 14
extension: .pdf
mime: application/pdf
words: 7445
sentence: 495
flesch: 48
cache: cache/jbi-8.pdf
txt: txt/jbi-8.txt
title:
  Climate Change and Biodiversity: Some Considerations in Forecasting Shifts in Species' Potential Distributions

summary:
  Ecological niche models, predicted geographic distributions, and climate change effects. Distribution model of the Volcano Rabbit (Romerolagus diazi) in central Mexico, showing raw predictions for (A) the present and (B) in 2050.


id: jbi-4717
author: Gobbett, David Lyon; Zerger, Andre
title: PointSampler: A GIS Tool for Point Intercept Sampling of Digital Images
date: 2014
pages: 5
extension: .pdf
mime: application/pdf
words: 2793
sentence: 164
flesch: 50
cache: cache/jbi-4717.pdf
txt: txt/jbi-4717.txt
summary:
  SamplePoint (Booth et al. 2006) is a tool for image classification using a point intercept method and supports a large number of cover classes. Where large numbers of images are captured, either across a spatial extent, or at at intervals as a time-series, it may be appropriate to utilize automated image analysis methods such as supervised classification.


id: jbi-4263
author: Coetzer, Willem
title: A new era for specimen databases and biodiversity information management in South Africa
date: 2012
pages: 11
extension: .pdf
mime: application/pdf
words: 5946
sentence: 287
flesch: 43
cache: cache/jbi-4263.pdf
txt: txt/jbi-4263.txt
summary:
  We present observations and a commentary on the inherited legacy and current state of biodiversity information management in South African natural history museums, and make recommendations for the future. In this article we consider some of the challenges faced by the South African biodiversity community with respect to biodiversity information management, and emphasize the importance of adopting a more systematic and rigorous approach to formal biodiversity information management in South African natural history museums.


id: jbi-6975
author: Lavariega, Mario César
title: An open-access platform for camera-trapping data
date: 2018
pages: 10
extension: .pdf
mime: application/pdf
words: 4856
sentence: 330
flesch: 52
cache: cache/jbi-6975.pdf
txt: txt/jbi-6975.txt
summary:
  Data Acquisition and management software for camera trap data: a case study from the TEAM network. Since analyses of wildlife data are essential to conservation and management efforts (Meffee et al. 2002), open access to biodiversity data becomes crucial (Molloy 2011, Thessen and Patterson 2011, Hanssen et al. 2014).


id: jbi-6507
title: Introducción a los Análisis Espaciales con Énfasis en Modelos de Nicho Ecológico
date: 2017
pages: 13
extension: .pdf
mime: application/pdf
words: 8291
sentence: 606
flesch: 49
cache: cache/jbi-6507.pdf
txt: txt/jbi-6507.txt
author:
  Cuervo-Robayo, Angela P.; Escobar, Luis E; Osorio-Olvera, Luis A.; Nori, Javier; Varela, Sara; Martinez-Meyer, Enrique; Velasquez-Tibata, Jorge; Rodriguez-Soto, Clarita; Munguia, Mariana; Castaneda-Alvarez, Nora P.; Lira-Noriega, Andres; Soley-Guardia, Mariano; Serra-Diaz, Josep M.; Peterson, A. Townsend

summary:
  4Departamento de Matemáticas de la Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México. Resumen.—En 2016 implementamos un sistema de seminarios de enseñanza, en formato de videos libres y accesibles desde internet, con la finalidad de dar a conocer de forma sencilla y en castellano, las bases conceptuales y aplicaciones de los modelos de nicho ecológico en estudios de ecología, conservación biológica, epidemiología y agrobiodviersidad, así como su implementación para el diseño de políticas públicas de los recursos naturales.


id: jbi-4300
author: Peterson, A. Townsend
title: Niche Modeling - Model Evaluation
date: 2012
pages: 1
extension: .pdf
mime: application/pdf
words: 212
sentence: 9
flesch: 32
cache: cache/jbi-4300.pdf
txt: txt/jbi-4300.txt
summary:
  The focus is on two solutions to the challenge of model evaluation: a simply cumulative binomial approach that can be used with binary model outputs, and partial ROC analysis, which can be used with continuous model outputs. Among these aspects is that of model evaluation or validation.


id: jbi-26
author: Hortal, Joaquín; Lobo, Jorge M
title: A synecological framework for systematic conservation planning
date: 2006
pages: 30
extension: .pdf
mime: application/pdf
words: 18874
sentence: 1319
flesch: 53
cache: cache/jbi-26.pdf
txt: txt/jbi-26.txt
summary:
  Elith, J., C. H. Graham, R. P. Anderson, M. Dudik, S. Ferrier, A. Guisan, R. J. Hijmans, F. Huettmann, J. R. Leathwick, A. Lehmann, J. Li, L. G. Lohmann, B. A. Loiselle, G. Manion, C. Moritz, M. Nakamura, Y. Nakazawa, J. M. M. Overton, A. T. Peterson, S. J. Phillips, K. Richardson, R. Scachetti-Pereira, R. E. Schapire, J. Soberon, S. Williams, M. S. Wisz, and N. E. Zimmermann. 2006. Unfortunately for this argument, the relevance of species in ecological processes is no better understood than is species distribution.


id: jbi-4126
title: Bridging the biodiversity data gaps: Recommendations to meet users’ data needs
date: 2013
pages: 18
extension: .pdf
mime: application/pdf
words: 10694
sentence: 661
flesch: 50
cache: cache/jbi-4126.pdf
txt: txt/jbi-4126.txt
author:
  Faith, Dan; Collen, Ben; Ariño, Arturo; Patricia Koleff, Patricia Koleff; Guinotte, John; Kerr, Jeremy; Chavan, Vishwas

summary:
  With the Global Biodiversity Information Facility (GBIF), we recently conducted a content needs assessment survey to consolidate and synthesize major user needs regarding biodiversity data. The recent call by scientists for new efforts to “map the biosphere” (Wheeler et al. 2012) also highlighted the importance of biodiversity data for addressing many basic research question in biodiversity science.


id: jbi-3664
author: Baskauf, Steven J
date: 2010
pages: 28
extension: .pdf
mime: application/pdf
words: 12190
sentence: 492
flesch: 29
cache: cache/jbi-3664.pdf
txt: txt/jbi-3664.txt
title:
  ORGANIZATION OF BIODIVERSITY RESOURCES BASED ON THE PROCESS OF THEIR CREATION AND THE ROLE OF INDIVIDUAL ORGANISMS AS RESOURCE RELATIONSHIP NODES

summary:
  The creation of occurrence resources follows a pattern which can be used as the basis for organizing both the metadata associated with those resources and the relationships among the resources. Because this system is based on the way occurrence resources are created, it connects the resources in a logically consistent way and associates metadata properties with resources in an efficient manner.


id: jbi-34
author: Sautter, Guido; Böhm, Klemens; Agosti, Donat
title: A combining approach to find all taxon names (FAT)
date: 2006
pages: 13
extension: .pdf
mime: application/pdf
words: 8528
sentence: 565
flesch: 63
cache: cache/jbi-34.pdf
txt: txt/jbi-34.txt
summary:
  We could exclude word sequences containing words with a meaning that cannot occur in taxonomic names. In this paper, we present computational linguistics techniques and evaluate how they can help to extract taxonomic names automatically.


id: jbi-4611
author: Talent, Nadia; Dickinson, Richard B.; Dickinson, Timothy A.
title: Character Selection During Interactive Taxonomic Identification: “Best Characters”
date: 2014
pages: 12
extension: .pdf
mime: application/pdf
words: 6355
sentence: 412
flesch: 52
cache: cache/jbi-4611.pdf
txt: txt/jbi-4611.txt
summary:
  The character set and character states are usually carefully chosen and limited in number to save space. A polyclave can be difficult to use correctly, such as by novices who make frequent errors, or for polythetic taxa which are distinguished by possessing a majority of a set of character states, rather than by required states (Morse 1971, 1975).


id: jbi-13218
date: 2020
pages: 11
extension: .pdf
mime: application/pdf
words: 6834
sentence: 437
flesch: 55
cache: cache/jbi-13218.pdf
txt: txt/jbi-13218.txt
author:
  Yañez, Carlos; Martín, Gerardo ; Osorio-Olvera, Luis; Escobar-Luján, Jazmín; Castaño-Quintero, Sandra; Chiappa-Carrara, Xavier; Martínez-Meyer, Enrique 

title:
  The Abundant Niche-centroid Hypothesis: Key Points About Unfilled Niches and the Potential Use of Supraspecfic Modeling Units

summary:
  We use the BAM components and configurations to exemplify situations in which distances to the niche centroid estimated from distributional data may and may not explain species abundances. Also, considering that M determines the set of regions and environments occupied by the species, the known set of presence records (G+) occur in geographic space (Go), so the associated environments η(G+) are already reduced by M. As a consequence, niche models that have been calibrated in an M region will frequently under-char- acterize the NF (Peterson and Soberón 2012), and the estimation of their centroid will be biased.


id: jbi-6707
author: Sainge, Moses Nsanyi; Onana, Jean-Michel; Nchu, Felix; Kenfack, David; Peterson, A. Townsend
title: Botanical Sampling Gaps Across the Cameroon Mountains
date: 2017
pages: 8
extension: .pdf
mime: application/pdf
words: 3679
sentence: 213
flesch: 60
cache: cache/jbi-6707.pdf
txt: txt/jbi-6707.txt
summary:
  km2, extending from Mt Cameroon (4095 m) and Mt Etinde (commonly called Small Mt Cameroon, 1474 m) on the coast, through a string of peaks, extending to the north and east into the interior (Figure 1). Diagrammatic representation of the Cameroon Mountain chain, extending from islands in the Gulf of Guinea to the coastal Mt Cameroon, and inland along the Cameroon-Nigeria border.


id: jbi-4801
author: Soberon, Jorge; Cavner, Jeff
title: Indices of Biodiversity Pattern Based on Presence-Absence Matrices: A GIS Implementation
date: 2015
pages: 13
extension: .pdf
mime: application/pdf
words: 7685
sentence: 463
flesch: 65
cache: cache/jbi-4801.pdf
txt: txt/jbi-4801.txt
summary:
  22-34 Finally, the covariance matrix between the species inhabiting sites j and k, and the covariance matrix between ranges of distribution of species h and i are, respectively: * * * * 1 1 1( ) 1 1 1( ) T T sites T T species S S S N N N ⎛ ⎞= − = −⎜ ⎟ Geographic range, turnover rate and scaling of species diversity.


id: jbi-4959
author: Wabuyele, Emily; Kang’ethe, Simon; Newton, Leonard E.
title: Digital Knowledge of Kenyan Succulent Flora and Priorities for Future Inventory and Documentation
date: 2016
pages: 11
extension: .pdf
mime: application/pdf
words: 5463
sentence: 278
flesch: 51
cache: cache/jbi-4959.pdf
txt: txt/jbi-4959.txt
summary:
  Data corresponding to succulent plant species were prioritised for digitisation as a thematic group of interest in conservation and trade across the region; as such, we estimate that 90% of succulent plant records at the EA have now been captured and are treated in this report. In addition, probable key sites of diversity and endemism for succulent plant species (the arid and semi-arid regions) are hard to access, both logistically and politically.


id: jbi-9786
author: Owens, Hannah Lois; Guralnick, Robert
title: climateStability: An R package to estimate climate stability from time-slice climatologies
date: 2019
pages: 6
extension: .pdf
mime: application/pdf
words: 3564
sentence: 207
flesch: 52
cache: cache/jbi-9786.pdf
txt: txt/jbi-9786.txt
summary:
  In particular, researchers have focused on climate stability as a key variable that can drive expected patterns of richness, phylogenetic diversity and functional diversity. Finally, climate stability is the product of individual climate variable stability estimates.


id: jbi-4094
author: Ariño, Arturo H.; Chavan, Vishwas; Faith, Daniel P.
title: Assessment of user needs of primary biodiversity data: Analysis, concerns, and challenges
date: 2013
pages: 35
extension: .pdf
mime: application/pdf
words: 12948
sentence: 558
flesch: 53
cache: cache/jbi-4094.pdf
txt: txt/jbi-4094.txt
summary:
  Options/Suboptions: No, I have not at all used GBIF mobilised data; No, not at all useful for my applications; Maybe, partially useful for my applications; Yes, completely useful for my applications; Please specify for what applications you use GBIF data: (Exclusive multiple choice) Q19. One-third of the respondents used GBIF data, either directly from the GBIF data portal, or similar access points.


id: jbi-13376
author: Simoes, Marianna; Romero-Alvarez, Daniel; Nuñez-Penichet, Claudia; Jiménez, Laura; E. Cobos, Marlon
title: General Theory and Good Practices in Ecological Niche Modeling: A Basic Guide
date: 2020
pages: 2
extension: .pdf
mime: application/pdf
words: 1041
sentence: 84
flesch: 59
cache: cache/jbi-13376.pdf
txt: txt/jbi-13376.txt
summary:
  Ecological niche modeling (ENM) and species distribution modeling (SDM) are sets of tools that allow the estimation of distributional areas on the basis of establishing relationships among known occur- rences and environmental variables. Seeking to reduce mistakes, improve standard- ization, ensure consistency, and provide training on the application of these tools, we provide basic guide- lines on the building of ecological niche models.


id: jbi-8189
title: Curso Modelado de Nicho Ecológico, Version 1.0
date: 2019
pages: 7
extension: .pdf
mime: application/pdf
words: 4014
sentence: 177
flesch: -17
cache: cache/jbi-8189.pdf
txt: txt/jbi-8189.txt
author:
  Peterson, A. Townsend; Anderson, Robert P; Cobos, Marlon E; Cuahutle, Martín; Cuervo-Robayo, Angela P; Escobar, Luis E; Fernández, Marc; Jiménez-García, Daniel; Lira-Noriega, Andrés; Lobo, Jorge M; Machado-Stredel, Fernando; Martínez-Meyer, Enrique; Nuñez-Penichet, Claudia; Nori, Javier; Osorio-Olvera, Luis; Rodríguez, María Teresa; Rojas-Soto, Octavio; Romero-Álvarez, Daniel; Soberón, Jorge; Varela, Sara; Yañez-Arenas, Carlos

summary:
  Palabras más frecuentes encontradas en las preguntas de los participantes del curso de Modelado de Nicho Ecológico. Resumen del curso de Modelado de Nicho Ecológico, Versión 1.0, incluyendo los temas principales, título espe- cífico, enlaces para las versiones en formato .pdf, .mp3, y .mp4,


id: jbi-9798
author: Peterson, A. Townsend; Soberón, Jorge; Ramsey, Janine; Osorio-Olvera, Luis
title: Co-occurrence Networks do not Support Identification of Biotic Interactions
date: 2020
pages: 10
extension: .pdf
mime: application/pdf
words: 6615
sentence: 394
flesch: 55
cache: cache/jbi-9798.pdf
txt: txt/jbi-9798.txt
summary:
  Data fitness for use in distribution modelling: Are species occurrence data in global online reposito- ries fit for modeling species distributions? We assess a body of work that has attempted to use co-occurrence networks to infer the existence and type of biotic interactions between species.


id: jbi-13302
author: Holt, Robert D.
title: Some thoughts about the challenge of inferring ecological interactions from spatial data.
date: 2020
pages: 6
extension: .pdf
mime: application/pdf
words: 4279
sentence: 242
flesch: 55
cache: cache/jbi-13302.pdf
txt: txt/jbi-13302.txt
summary:
  They use an anal- ogy with physics to understand ecology (in their Box 1), and state that fundamental interactions in physics are ‘direct’, whereas other interactions are ‘indirect’. In the former case, the epsilon of Stephens et al. indicates positive interactions, yet experiments show negative interactions.


id: jbi-4326
author: Rödder, Dennis; Engler, Jan O.
date: 2012
pages: 11
extension: .pdf
mime: application/pdf
words: 6266
sentence: 310
flesch: 45
cache: cache/jbi-4326.pdf
txt: txt/jbi-4326.txt
title:
  DISENTANGLING INTERPOLATION AND EXTRAPOLATION UNCERTAINTIES IN SPECIES DISTRIBUTION MODELS: A NOVEL VISUALIZATION TECHNIQUE FOR THE SPATIAL VARIATION OF PREDICTOR VARIABLE COLINEARITY

summary:
  Assume that an ENM is developed within one part of the study region (training area, black bar) and subsequently projected onto the rest of the gradient. Using species distribution models in palaeobiogeography: A matter of data, predictors and concepts.


id: jbi-14782
author: Soberón, Jorge; Cobos, Marlon E.; Nuñez-Penichet, Claudia
title: Visualizing species richness and site similarity from presence-absence matrices
date: 2021
pages: 8
extension: .pdf
mime: application/pdf
words: 5160
sentence: 268
flesch: 56
cache: cache/jbi-14782.pdf
txt: txt/jbi-14782.txt
summary:
  Considering how the ran- domization is done, before starting the process, we broke any potential geographic structure remaining in the PAM (where closer rows are also closer cells in the geography) by rearranging randomly the rows (which represent geographic cells) but maintaining the identity of these cells in the results. The two cases are: 1) a positive mini- mum covariance when comparing communities per site (grid cells in our case); and 2) the case with a negative minimum covariance.


id: jbi-13384
title: Presence-only and Presence-absence Data for Comparing Species Distribution Modeling Methods
date: 2020
pages: 12
extension: .pdf
mime: application/pdf
words: 7291
sentence: 437
flesch: 65
cache: cache/jbi-13384.pdf
txt: txt/jbi-13384.txt
author:
  Elith, Jane; Graham, Catherine; Valavi, Roozbeh; Abegg, Meinrad; Bruce, Caroline; Ferrier, Simon; Ford, Andrew; Guisan, Antoine; Hijmans, Robert J.; Huettmann, Falk; Lohmann, Lucia; Loiselle, Bette; Moritz, Craig; Overton, Jake; Peterson, A. Townsend; Phillips, Steven; Richardson, Karen; Williams, Stephen; Wiser, Susan K.; Wohlgemuth, Thomas; Zimmermann, Niklaus E.

summary:
  The regions show useful vari- ation in the amount of species data per region, with tens to thousands of PO records per species, and 102 to 19 120 PA evaluation sites (Table 1 and detailed summaries per region in Supplementary Information 2). Top left: maps of species data, top right: an interactive map with PA site locations; Bottom left: density plot showing the distribution of PO data along one environmental gradient, compared with that of random points from the region; Bottom right: pairwise correlations between variable.


id: jbi-5008
author: Peterson, A. Townsend; Ingenloff, Kate
title: Biodiversity Informatics Training Curriculum, version 1.2
date: 2016
pages: 10
extension: .pdf
mime: application/pdf
words: 3277
sentence: 228
flesch: -10
cache: cache/jbi-5008.pdf
txt: txt/jbi-5008.txt
summary:
  Writing Proposals Biodiversity Data Capture and Initial Enrichment  Biodiversity Data Capture  Welcome to Ghana  Symbiota  Software Highlight: Specify  Data Capture: Strategy  Data Capture from Images  Data Capture: Demonstration 


id: jbi-12060
author: Peterson, A. Townsend; Soberón, Jorge; Ramsey, Janine; Osorio-Olvera, Luis
title: Response to Stephens et al. (2019)
date: 2020
pages: 2
extension: .pdf
mime: application/pdf
words: 1045
sentence: 46
flesch: 45
cache: cache/jbi-12060.pdf
txt: txt/jbi-12060.txt
summary:
  Interpretation as actual interactions—and determining types of in- teractions—requires further information that is gen- erally unavailable from simple occurrence data. Similarly, for pollination, or any other type of ecological micro interaction.


id: jbi-7108
author: Asase, Alex; Schwinger, Gladys O
title: Assessment of biodiversity data holdings and user data needs for Ghana
date: 2018
pages: 11
extension: .pdf
mime: application/pdf
words: 5784
sentence: 339
flesch: 47
cache: cache/jbi-7108.pdf
txt: txt/jbi-7108.txt
summary:
  Biodiversity data include data on species inventories, distributions, images, sounds, specimens, and ecological interactions, as well as descriptions of datasets (i.e., metadata) (Costello et al., 2013). Biodiversity data are basically of two kinds (i.e., primary and secondary), and can be numerical, categorical (e.g., species or place names), or media- based (Costello et al., 2013).


id: jbi-6744
author: Lowenberg Neto, Peter
title: A metric to quantify analogous conditions and rank environmental layers
date: 2018
pages: 16
extension: .pdf
mime: application/pdf
words: 5267
sentence: 300
flesch: 54
cache: cache/jbi-6744.pdf
txt: txt/jbi-6744.txt
summary:
  It is expected that heterogeneous layers would generate better correlational geographic distributional predictions than analogous variables, even though this hypothesis remains untested. peter.lowenberg@unila.edu.br Abstract.—Analogous conditions in environmental variables are expected because environments are spatially autocorrelated and often present similar combinations over geographic space.


id: jbi-4914
author: Idohou, Rodrigue; Arino, Arturo; Assogbadjo, Achille; Glele Kakai, Romain; Sinsin, Brice
date: 2015
pages: 11
extension: .pdf
mime: application/pdf
words: 4971
sentence: 302
flesch: 58
cache: cache/jbi-4914.pdf
txt: txt/jbi-4914.txt
title:
  DIVERSITY OF WILD PALMS (ARECACEAE) IN THE REPUBLIC OF BENIN: FINDING THE GAPS IN THE NATIONAL INVENTORY COMBINING FIELD AND DIGITAL ACCESSIBLE KNOWLEDGE

summary:
  Most ecosystems hosting palm species in the country appear to be well sampled, except some sections in the northern and western fringes, as well as remote areas with potentially difficult accessibility as seen in low road density (Figure 3), which do not seem to lack records but show low completeness. Decision table for levels of knowledge of palm species across Benin.


id: jbi-15016
title: ENM2020: A Free Online Course and Set of Resources on Modeling Species' Niches and Distributions
date: 2022
pages: 9
extension: .pdf
mime: application/pdf
words: 4386
sentence: 158
flesch: 0
cache: cache/jbi-15016.pdf
txt: txt/jbi-15016.txt
author:
  Peterson, A. Townsend; Aiello-Lammens, Matthew; Amatulli, Giuseppe; Anderson, Robert; Cobos, Marlon; Diniz-Filho, José Alexandre; Escobar, Luis; Feng, Xiao; Franklin, Janet; Gadelha, Luiz; Georges, Damien; Guéguen, M; Gueta, Tomer; Ingenloff, Kate; Jarvie, Scott; Jiménez, Laura; Karger, Dirk; Kass, Jamie; Kearney, Michael; Loyola, Rafael; Machado-Stredel, Fernando; Martínez-Meyer, Enrique; Merow, Cory; Mondelli, Maria Luiza; Mortara, Sara; Muscarella, Robert; Myers, Corinne; Naimi, Babak; Noesgaard, Daniel; Ondo, Ian; Osorio-Olvera, Luis; Owens, Hannah; Pearson, Richard; Pinilla-Buitrago, Gonzalo; Sánchez-Tapia, Andrea; Saupe, Erin; Thuiller, Wilfried; Varela, Sara; Warren, Dan; Wieczorek, John; Yates, Katherine; Zhu, Gengping; Zuquim, Gabriela; Zurell, Damaris

summary:
  BAM scenario exercises Video ATP Pdf -- Question and answer Video MC, FMS, MP, ATP -- Materials Special discussion: Extent and Resolution Video MC, JS, ATP -- EcoClimate ALGORITHMS Algorithms / Relation to Theory† Video JF Pdf Hastie, Elith, Elith06 Un Solo Díos Video ATP Pdf Materials Question and answer Video MC, ATP -- Paper on uses, Zhu. BAM and M and model success - What you can and cannot model Video ATP Pdf BAM, Literature.


id: jbi-21511
author: Campbell, Peter
title: Interpreting and Georeferencing the Concept of “Near” in Biodiversity Records
date: 2024
pages: 11
extension: .pdf
mime: application/pdf
words: 5593
sentence: 286
flesch: 46
cache: cache/jbi-21511.pdf
txt: txt/jbi-21511.txt
summary:
  An intermediate Voronoi diagram with one Voronoi polygon per point, but several Voronoi polygons per locality. Each unique fire station is labeled with a letter and has a corresponding Voronoi polygon.


id: jbi-15985
author: Cobos, Marlon E.; Peterson, A. Townsend
date: 2022
pages: 9
extension: .pdf
mime: application/pdf
words: 4856
sentence: 277
flesch: 50
cache: cache/jbi-15985.pdf
txt: txt/jbi-15985.txt
title:
  Detecting Signals of Species’ Ecological Niches in Results of Studies with Defined Sampling Protocols: Example Application to Pathogen Niches

summary:
  Pathogen niche is equal to host niche 12–26 700–2800 T: 5.44 P: 122,500 0.52 Pathogen 2 Pathogen niche has the same size as host niche but with changed position 14–28 800–2900 T: 5.44 P: 122,500 0.38 Pathogen 3 Pathogen niche changed in position and size (smaller) compared to host niche 13–22 900–2600 T: 2.25 P: 8,277


id: jbi-5860
author: Asase, Alex; Peterson, A. Townsend
title: Completeness of Digital Accessible Knowledge of the Plants of Ghana
date: 2016
pages: 11
extension: .pdf
mime: application/pdf
words: 4510
sentence: 280
flesch: 57
cache: cache/jbi-5860.pdf
txt: txt/jbi-5860.txt
summary:
  Recent efforts within Ghana have digitized >90% of primary biodiversity data records associated with specimen sheets in Ghanaian herbaria; additional herbarium data are available from other institutions via biodiversity informatics initiatives such as the Global Biodiversity Information Facility. These initiatives have contributed to massive accumulation and serving of primary biodiversity data records via the Internet: e.g., GBIF currently serves >648M primary data records on its data portal (accessed 13 May 2016).


id: jbi-15581
author: Saeedi, Hanieh; Brandt, Angelika; Jacobsen, Nils L.
date: 2022
pages: 17
extension: .pdf
mime: application/pdf
words: 10450
sentence: 670
flesch: 65
cache: cache/jbi-15581.pdf
txt: txt/jbi-15581.txt
title:
  Biodiversity and distribution of Isopoda and Polychaeta along the Northwestern Pacific and the Arctic Ocean

summary:
  Rarefac‑ tion (ES15) showed that highest species richness was around the Philippines, Sea of Japan, Yellow Sea, and the AO (Fig. 1). Polychaetes with unknown pelagic larvae showed higher species richness in the AO as well the Sea of Japan and the Yellow Sea (Fig. S8).


id: jbi-5053
author: Ganglo, Jean Cossi; Kakpo, Sunday Berlioz
date: 2016
pages: 17
extension: .pdf
mime: application/pdf
words: 7112
sentence: 334
flesch: 58
cache: cache/jbi-5053.pdf
txt: txt/jbi-5053.txt
title:
  Completeness of Digital Accessible Knowledge of Plants of Benin and Priorities for Future Inventory and Data Discovery

summary:
  Finally, we explored, in a preliminary manner, the impacts of absence of roads, waterways, and protected areas on data completeness. To be more consistent with the status and reality of data completeness of the country, we considered grid cells as best- known when N ≥ 200 records and C ≥ 0.8.


id: jbi-4955
date: 2015
pages: 21
extension: .pdf
mime: application/pdf
words: 10401
sentence: 641
flesch: 56
cache: cache/jbi-4955.pdf
txt: txt/jbi-4955.txt
author:
  Lima-Ribeiro, Matheus Souza; Varela, Sara; González-Hernández, Javier; de Oliveira, Guilherme; Diniz-Filho, José Alexandre F.; Terribile, Levi Carina

title:
  EcoClimate: a database of climate data from multiple models for past, present, and future for macroecologists and biogeographers

summary:
  This suite of methods and ideas has been applied to diverse research purposes: guiding discovery of populations of known (Bourg et al., 2005; Guisan et al., 2006) and unknown (Raxworthy et al., 2003) species; understanding distributional dynamics under past (Banks et al., 2008a; 2008b) and future (Dormann, 2007; Anderson, 2013) climates; anticipating climate change impacts on agricultural (Fraga et al., 2013) and natural (Nabout et al., 2011) extraction; mapping invasion risk (Peterson, 2003; Jiménez-Valverde et al., 2011), pest distributions (Venette et al., 2010; Estay et al., 2014), and disease trasmission (Peterson, 2014); estimating population parameters (Tôrres et al., 2012; Lima-Ribeiro and Diniz- Filho, 2013; Thuiller et al., 2014), species richness (Wisz and Rahbeck, 2007; Lima- Ribeiro et al., 2013b), and community composition (Pellissier et al., 2012); analyzing biotic interactions (Anderson et al., 2002; Wheeler et al., 2015); illuminating patterns and processes of diversification and speciation (Silva et al., 2014); characterizing dispersal (Génard and Lescourret, 2013; Saltré et al., 2015); highlighting extinction (Nogués-Bravo et al., 2008; Lima-Ribeiro et al., 2013a); testing niche conservatism (Martínez-Meyer et al., 2004; 2006; Peterson and Nyári, 2007; Jakob et al., 2010) and phylogeographic hypotheses (Collevatti et al., 2013b; 2015; Alvarado-Serrano and Knowles, 2014); establishing historical refugia (Waltari et al., 2007; Terribile et al., 2012); identifying biodiversity hotspots (Carnaval and Moritz, 2008; Carnaval et al., 2009); choosing appropriate areas for biodiversity conservation (Nobrega and De Marco, 2011; Williams et al., 2013) and translocation (Martínez-Meyer et al., 2006; Richmond et al., 2010); etc. 1-­‐12   climate change; to understand past extinction events (Lima-Ribeiro et al., 2013a); and to test hypotheses concerning population dynamics (Barrientos et al., 2014), evolutionary processes (Araújo et al., 2013; Saupe et al., 2014), and ecological dynamics (Martínez-Meyer et al., 2004; Martínez-Meyer and Peterson, 2006).


id: jbi-16271
title: rangemap: An R Package to Explore Species' Geographic Ranges
date: 2022
pages: 8
extension: .pdf
mime: application/pdf
words: 4124
sentence: 284
flesch: 51
cache: cache/jbi-16271.pdf
txt: txt/jbi-16271.txt
author:
  Cobos, Marlon E.; Barve, Vijay ; Barve, Narayani; Jiménez-Valverde, Alberto; Nuñez-Penichet, Claudia

summary:
  Data required The main input for analysis functions is a set of occurrence data (geographic coordinates) in the form of a “data.frame”. Visualization tools included in the package help to produce simple, high-quality representations of occurrence data and figures summarizing resulting ranges in geographic and environmental spaces.


id: jbi-11989
author: Dallas, Tad A.; Santini, Luca ; Decker, Robin ; Hastings, Alan
title: Weighing the Evidence for the Abundant-Center Hypothesis
date: 2020
pages: 11
extension: .pdf
mime: application/pdf
words: 7619
sentence: 467
flesch: 52
cache: cache/jbi-11989.pdf
txt: txt/jbi-11989.txt
summary:
  Here, Table 1: A review of existing support for the abundant-center hypothesis suggests that approximately 20% of species demonstrate a relationship between species density and distance to a species geographic range or climatic niche center. Reflecting boundaries such as impassable streams serve may influence the spatial distribution of species density by increasing species densities at barriers, and by not allowing access to suitable geographic areas beyond the dis- persal barriers (Nislow et al. 2011).


id: jbi-7036
author: Merckx, Jonas; Van Roie, Martijn; Gómez-Zurita, Jesús; Dekoninck, Wouter
date: 2018
pages: 11
extension: .pdf
mime: application/pdf
words: 5979
sentence: 571
flesch: 57
cache: cache/jbi-7036.pdf
txt: txt/jbi-7036.txt
title:
  From theory to practice: a photographic inventory of museum collections to optimize collection management

summary:
  We describe the results of the digitization of Calligrapha specimens in the form of a specimen list and dorsal photographs of the specimens, as well as an assess- ment of the monetary cost avoided with the use of specimen digitization and give an estimation of the time needed for each step of the process. specimen digitization a valuable tool in facilitating museum collection management.


id: jbi-14758
author: Zabihi, Khodabakhsh; Huettmann, Falk; Young, Brian
date: 2021
pages: 19
extension: .pdf
mime: application/pdf
words: 11399
sentence: 650
flesch: 56
cache: cache/jbi-14758.pdf
txt: txt/jbi-14758.txt
title:
  Predicting multi-species bark beetle (Coleoptera: Curculionidae: Scolytinae) occurrence in Alaska: First use of open access big data mining and open source GIS to provide robust inference and a role model for progress in forest conservation

summary:
  Elevation showed a different pattern from other predictors: in all three models, areas at elevations <2000 m and >4000 m favored bark beetle presence, whereas elevations of 2000-4000 m was not occupied by bark beetle species. In this sense, the common, individual-based approach of modeling and mapping spatial distributions of bark beetle species may not provide comprehensive information required for efficient forest management.


id: jbi-4124
date: 2013
pages: 79
extension: .pdf
mime: application/pdf
words: 20545
sentence: 966
flesch: 50
cache: cache/jbi-4124.pdf
txt: txt/jbi-4124.txt
author:
  Gaiji, Samy; Chavan, Vishwas; Ariño, Arturo H.; Otegui, Javier; Hobern, Donald; Sood, Rajesh; Robles, Estrella

title:
  Content assessment of the primary biodiversity data published through GBIF network: Status, challenges and potentials

summary:
  Valid OCC Not valid OCC Null value % RAW Valid Matching 63,9% -- -- 63,9% Not matching -- 0,1% 8,6% 8,7% Not valid Matching -- 0,2% -- 0,2% Not matching 0,1% -- 0,4% 0,5% Null Matching -- -- 17,7% 17,7% Not matching 5,0% 3,9% -- 8,9% Total 69,1% 4,3% 26,7% 100,0% 31% Table 9. Zenaida macroura 2,270,891 (+4,9%) 0.7% 99.9% Sturnus vulgaris 2,171,136 (+17,2%) 0.7% 99.7% Passer domesticus 2,029,427 (+7.2%) 0.6% 99.0% Cardinalis cardinalis 1,779,316 (-8.9%) 0.5% 99.9% Picoides pubescens 1,776,269 (+6.2%) 0.5% 99.9% Junco hyemalis 1,731,413 (-0.2%) 0.5% 99.3%


id: jbi-24159
date: 2025
pages: 11
extension: .pdf
mime: application/pdf
words: 6933
sentence: 312
flesch: 46
cache: cache/jbi-24159.pdf
txt: txt/jbi-24159.txt
author:
  Cobos, Marlon; Carrion Bonilla, Carlos; Burneo, Santiago; Cook, Joseph; Dunnum, Jonathan; Frank, Lexi; Grover, Mackenzie; Hey, Alexander; Larsen, Peter; Wiens, Benjamin; Camacho, Alejandra; Colella, Jocelyn

title:
  Field+Genomics Workshop: an initiative to build Nanopore sequencing capacity in field-based host-pathogen research

summary:
  Rudzki, E. N., Kuebbing, S. E., Clark, D. R., Gharaibeh, B., Janecka, M. J., Kramp, R., Kohl, K. D., Mastals- ki, T., Ohmer, M. E. B., Turcotte, M. M., and Rich- ards-Zawacki, C. L. (2022). On Day 2, workshop participants observed the process.


id: jbi-24329
title: letsRept: An R package to access the Global Reptile Database and facilitate taxonomic harmonization
date: 2025
pages: 24
extension: .pdf
mime: application/pdf
words: 10047
sentence: 475
flesch: 43
cache: cache/jbi-24329.pdf
txt: txt/jbi-24329.txt
author:
  dos Santos Vieira de Alencar, João Paulo; Liedtke, H. Cristoph; Meiri, Shai; Roll, Uri; Uetz, Peter; Nori, Javier

summary:
  Its main functions allow users to retrieve the most up-to-date taxonomic information in real time, to compare lists of species names to current nomenclature, and to detect names that have been changed by either lumping or splitting, all through web scraping techniques. This is termed a ‘Linnean Shortfall’, which describes the discrepancy between the number of species that exist and the number of species that were formally described and are known to science to date (Brown and Lomolino, 1998; Hortal et al., 2015).


id: jbi-13402
author: Stephens, Christopher Rhodes
title: Can We Infer Species Interactions from Co-occurrence Patterns? A Reply to Peterson et al. (2020)
date: 2020
pages: 4
extension: .pdf
mime: application/pdf
words: 2615
sentence: 108
flesch: 52
cache: cache/jbi-13402.pdf
txt: txt/jbi-13402.txt
summary:
  The properties that Peterson et al. question are all well-known attributes of this diagnostic. Our key assertion, again, is that geographic co-occurrence is a necessary but not sufficient condition for such biotic interactions to be present.


id: jbi-22655
author: Luna, Sergio; Peña-Peniche, Alexander; Mendoza-Alfaro, Roberto
title: Species distribution model accuracy is strongly influenced by the choice of calibration area
date: 2024
pages: 13
extension: .pdf
mime: application/pdf
words: 8457
sentence: 572
flesch: 50
cache: cache/jbi-22655.pdf
txt: txt/jbi-22655.txt
summary:
  Key words: species distribution models, ecological niche, calibration area, model accuracy, virtual species, simulations, Maxent Introduction Species distribution models (SDM) are widely used tools in ecology and conservation aimed at pre- dicting the potential distribution of a species based on its environmental requirements and occurrence data (Peterson and Soberón 2012). The present study has demonstrated that the area of calibration is one of the most important factors affecting the functional ac- curacy of species distribution models using Maxent.


id: jbi-6522
author: Rees, Tony; Vandepitte, Leen; Decock, Wim; Vanhoorne, Bart
title: IRMNG 2006–2016: 10 Years of a Global Taxonomic Database
date: 2017
pages: 44
extension: .pdf
mime: application/pdf
words: 25599
sentence: 855
flesch: 55
cache: cache/jbi-6522.pdf
txt: txt/jbi-6522.txt
summary:
  Such names are retained in IRMNG since they may appear in published literature and/or other taxonomic data compila- tions and may be required for correct assignment of accompanying information; whenever possible they are pointed to the current accepted name for the same taxon, when known. A small number of genus names (approx. 10,000) has entered IRMNG from sources not considered “trusted” in this sense, such as museum databases or third-party compilations, and do not match entries in major nomenclators on a first pass; such names are identified as candidates for further investigation and will either be accepted or rejected for continued IRMNG use in due course.


id: jbi-22332
date: 2024
pages: 4
extension: .pdf
mime: application/pdf
words: 2612
sentence: 85
flesch: 12
cache: cache/jbi-22332.pdf
txt: txt/jbi-22332.txt
author:
  Mastretta-Yanes, Alicia; Suárez, Sofía; Jordan, Rebecca; Hoban, Sean; da Silva, Jessica M.; Castillo-Reina, Luis; Heuertz, Myriam; Ishihama, Fumiko; Köppä, Viktoria; Laikre, Linda; MacDonald, Anna J.; Mergeay, Joachim; Paz-Vinas, Ivan; Segelbacher, Gernot; Knapps, Alicia; Rakoczy, Henry; Weiler, Amelie; Atsaves, Angelica; Cullmann, Kira; Bagnato, Simone; Forester, Brenna R.

title:
  Guideline Materials and Documentation for the Genetic Diversity Indicators of the Monitoring Framework for the Kunming-Montreal Global Biodiversity Framework

summary:
  Monitoring status and trends in genetic diversity for the Convention on Biological Diversity: An ongoing assess- ment of genetic indicators in nine countries. Multinational evaluation of genetic diversity indicators for the Kunming-Montreal Global Biodiversity Framework.


id: jbi-24398
author: Gamboa, Sara
title: Review - The Game of Species. An Introduction to Biodiversity.
date: 2025
pages: 1
extension: .pdf
mime: application/pdf
words: 710
sentence: 31
flesch: 45
cache: cache/jbi-24398.pdf
txt: txt/jbi-24398.txt
summary:
  López ex- plains why biodiversity is unevenly distributed across the planet, why extinction is as important as speciation, and why ecological interactions create functional rather than merely numerical diversity. Pelagic Publishing, 2022 Sara Gamboa MapasLab, Ecology and Animal Biology Department, University of Vigo, Spain The Game of Species: An Introduction to Biodiversity offers a distinctive synthesis of evolutionary and ecologi- cal thought, presented through the powerful metaphor of a game.


id: jbi-21810
title: Addressing multiple facets of bias and uncertainty in continental scale biodiversity databases
date: 2024
pages: 22
extension: .pdf
mime: application/pdf
words: 12349
sentence: 598
flesch: 56
cache: cache/jbi-21810.pdf
txt: txt/jbi-21810.txt
author:
  Marchetto, Elisa; Livornese, Martina ; Sabatini, Francesco Maria ; Tordoni, Enrico; Da Re, Daniele ; Lenoir, Jonathan ; Testolin, Riccardo ; Bacaro, Giovanni ; Cazzolla Gatti, Roberto ; Chiarucci, Alessandro ; Foody, Giles M. ; Gábor, Lukáš ; Groom, Quentin ; Iaria, Jacopo ; Malavasi, Marco ; Moudr´y, V´ıtˇezslav ; Santovito, Diletta ; Šímová, Petra; Zannini, Piero ; Rocchini, Duccio 

summary:
  Sabatini, F. M., J. Lenoir, T. Hattab, E. A. Arnst, M. Chytrý, J. Marchetto et al. – Addressing Multiple Facets of Bias and Uncertainty in Continental-Scale Biodiversity Databases 71 Dengler, P. De Ruffray, S. M. Hennekens, U. Jandt, F. Jan- sen, B. Jiménez‐Alfaro, J. Kattge, A. Levesley, V. D. Pillar, O. Purschke, B. Sandel, F. Sultana, T. Aavik, S. Aćić, A. T. R. Acosta, E. Agrillo, M. Alvarez, I. Apostolova, M. A. S. Arfin Khan, L. Arroyo, F. Attorre, I. Aubin, A. Banerjee, M. Bauters, Y. Bergeron, E. Bergmeier, I. Biurrun, A. D. Bjorkman, G. Bonari, V. Bondareva, J. Brunet, A. Čarni, L. Casella, L. Cayuela, T. Černý, V. Chepinoga, J. Csiky, R. Ćušterevska, E. De Bie, A. L. De Gasper, M. De Sanctis, P. Dimopoulos, J. Dolezal, T. Dziuba, M. A. E. M. El‐Sheikh, B. Enquist, J. Ewald, F. Fazayeli, R. Field, M. Finckh, S. Gachet, A. Galán‐de‐Mera, E. Garbolino, H. Gholizadeh, M. Giorgis, V. Golub, I. G. Alsos, J. Grytnes, G. R. Guer- in, A. G. Gutiérrez, S. Haider, M. Z. Hatim, B. Hérault, G. Hinojos Mendoza, N. Hölzel, J. Homeier, W. Hubau, A. Indreica, J. A. M. Janssen, B. Jedrzejek, A. Jentsch, N. Jür- gens, Z. Kącki, J. Kapfer, D. N. Karger, A. Kavgacı, E. Ke- arsley, M. Kessler, L. Khanina, T. Killeen, A. Korolyuk, H. Kreft, H. S. Kühl, A. Kuzemko, F. Landucci, A. Lengyel, F. Lens, D. V. Lingner, H. Liu, T. Lysenko, M. D. Mahecha, C. Marcenò, V. Martynenko, J. E. Moeslund, A. Monteagudo Mendoza, L. Mucina, J. V. Müller, J. Munzinger, A. Naqine- zhad, J. Noroozi, A. Nowak, V. Onyshchenko, G. E. Over- beck, M. Pärtel, A. Pauchard, R. K. Peet, J. Peñuelas, A. Pérez‐Haase, T. Peterka, P. Petřík, G. Peyre, O. L. Phillips, V. Prokhorov, V. Rašomavičius, R. Revermann, G. Rivas‐ Torres, J. S. Rodwell, E. Ruprecht, S. Rūsiņa, C. Samimi, M. Schmidt, F. Schrodt, H. Shan, P. Shirokikh, J. Šibík, U. Šilc, P. Sklenář, Ž. Škvorc, B. Sparrow, M. G. Sperandii, Z. Stančić, J. Svenning, Z. Tang, C. Q. Tang, I. Tsiripidis, K. A. Vanselow, R. Vásquez Martínez, K. Vassilev, E. Vélez‐ Martin, R. Venanzoni, A. C. Vibrans, C. Violle, R. Virtanen, H. Von Wehrden, V. Wagner, D. A. Walker, D. M. Waller, H. Wang, K. Wesche, T. J. S. Whitfeld, W. Willner, S. K. Wiser, T. Wohlgemuth, S. Yamalov, M. Zobel, and H. Bru- elheide. 2021b. Lobo, J. M., J. Hortal, J. L. Yela, A. Millán, D. Sánchez-Fernán- dez, E. García-Roselló, J. González-Dacosta, J. Heine, L. González-Vilas, and C. Guisande.


id: jbi-23725
author: Islam, Shariful; Castaneda-Guzman, Mariana; Soler-Tovar, Diego; Escobar, Luis
title: Ecological Niche Modeling Applications to Infectious Diseases
date: 2025
pages: 24
extension: .pdf
mime: application/pdf
words: 11104
sentence: 641
flesch: 42
cache: cache/jbi-23725.pdf
txt: txt/jbi-23725.txt
summary:
  Campos et al. 2023; Feng et al. 2019b; Lippi et al. 2023a; Valavi et al. 2022). For example, Romero-Alvarez et al. (2023) assessed the potential spread of Oropouche virus in humans, and Escobar et al. (2017) identified areas of transmission risk for Heterosporis, a fish disease caused by the microsporidian parasite Heterosporis sutherlandae.


id: jbi-16441
title: Best Practices for Data Management in Citizen Science - An Indian Outlook
date: 2022
pages: 23
extension: .pdf
mime: application/pdf
words: 15872
sentence: 873
flesch: 50
cache: cache/jbi-16441.pdf
txt: txt/jbi-16441.txt
author:
  Vattakaven, Thomas; Barve, Vijay ; Ramaswami, Geetha; Singh, Priya; Jagannathan, Suneha; Dhandapani, Balasubramanian

summary:
  Planning for Data Quality Assurance The credibility and quality of citizen science data is often questioned even though recent studies have challenged this view (e.g., Barve 2014). Regular backup of data with multiple copies in multiple locations and a con- sistent preservation policy across sites is essential for the security and integrity of citizen science data.


id: jbi-15483
author: Rocha, Tainá; Vale, Mariana M.; Lima-Ribeiro, Matheus S.
title: Global land-use and land-cover data for ecologists: Historical, current, and future scenarios
date: 2021
pages: 11
extension: .pdf
mime: application/pdf
words: 6878
sentence: 461
flesch: 66
cache: cache/jbi-15483.pdf
txt: txt/jbi-15483.txt
summary:
  36(2): 601-616. doi:10.1007/s10980-020-01152-z Chase, J. M., S.A. Blowes, T. M Knight, K. Gerstner, and F. May, F. 2020. Change, 109: 1-4. doi:10.1007/s10584-011- 0157-y. Zabel, F., Delzeit, R., Schneider, J. M., Seppelt, R., Maus- er, W., and Václavík, T. 2019.


id: jbi-20516
title: The IBdata Web System for Biological Collections: Design Focused on Usability
date: 2024
pages: 12
extension: .pdf
mime: application/pdf
words: 8067
sentence: 381
flesch: 51
cache: cache/jbi-20516.pdf
txt: txt/jbi-20516.txt
author:
  Murguía-Romero, Miguel; Serrano-Estrada, Bernardo; Salazar, Gerardo A.; Sánchez-González, Gerardo E.; Melo Samper Palacios, Ubaldo; Gernandt, David S.; Magallón, Susana; Sánchez-Cordero, Víctor

summary:
  In recent years, user interface design has benefited from the concept of usability (Bevan et al., 2016; ISO, 2018), understood as the degree to which specific users can use a system, product, or service to achieve specific objectives with effectiveness, efficiency, and satisfaction. User interface design (UI design)


id: jbi-17593
author: Vignoles, Anais
title: Guide francophone pour la modélisation de niches écologiques
date: 2022
pages: 29
extension: .pdf
mime: application/pdf
words: 19464
sentence: 1285
flesch: 61
cache: cache/jbi-17593.pdf
txt: txt/jbi-17593.txt
summary:
  Escobar et al., 2014; Alkishe et al., 2020; Nuñez-Penichet et al., 2021a), les mécanismes de macroévolution des espèces (e.g., Saupe et al., 2019), la paléoécologie et paléo-distribution d’espèces fossiles (e.g., Myers et al., 2015; Gibert, Vignoles et al., 2022), la diffusion de maladies via des vecteurs animaux (e.g., Sweeney et al., 2006; Escobar et al., 2017; Marques et al., 2020, 2021), l’impact du changement climatique sur les espèces animales ou végétales (e.g., Warren et al., 2014; Ashraf et al., 2017), ou encore les relations culture- environnement chez les chasseurs-cueilleurs du Paléolithique (e.g., Banks et al., 2006, 2009, 2011, 2021; Vignoles et al., 2021). Dans ce cadre, il est possible d’établir au moins quatre configurations du diagramme BAM (Peterson et al., 2011; Saupe et al., 2012; Figure 4): i) la configuration classique, dans laquelle


id: jbi-24120
author: Li, Wen; Peng, Yu; Zhang, Xiaoyue
date: 2025
pages: 23
extension: .pdf
mime: application/pdf
words: 11797
sentence: 737
flesch: 62
cache: cache/jbi-24120.pdf
txt: txt/jbi-24120.txt
title:
  Functional diversity rather than species diversity can be accurately assessed by remote sensing in sandy grassland

summary:
  The resulting models exhibited high coefficients of de- termination (R2) and significant relationships between the indices and plant diversity indices (P < 0.05), indicating their potential as optimal indices (Table 1). Model validation Using the six identified optimal spectral and texture indices listed in Table 1, plant diversity indices were cal- culated for the 48 model validation plots using the spectral and texture dataset.


id: jbi-5886
author: Kelly, Maggi
date: 2016
pages: 23
extension: .pdf
mime: application/pdf
words: 13303
sentence: 831
flesch: 58
cache: cache/jbi-5886.pdf
txt: txt/jbi-5886.txt
title:
  Rescuing and Sharing Historical Vegetation Data for Ecological Analysis: The California Vegetation Type Mapping Project

summary:
  Conlisk et al. (2012) used VTM plot data and herbarium records with the species distribution modeling algorithm Maxent (Phillips et al. 2006) to find locations and carrying capacities of metapopulation patches of Quercus engelmannii in eastern San Diego County. Currently, most papers using VTM plot data explore the full complement of scale and detail.


id: jbi-21742
author: Arias-Giraldo, Luis F.; Cobos, Marlon E.
date: 2024
pages: 15
extension: .pdf
mime: application/pdf
words: 8517
sentence: 565
flesch: 55
cache: cache/jbi-21742.pdf
txt: txt/jbi-21742.txt
title:
  enmpa: An R package for ecological niche modeling using presence-absence data and generalized linear models

summary:
  Ecological niche modeling helps in this task, and this contribution introduces enmpa, an R package that facilitates calibration of ecological niche models via GLM. kuenm: an R package for detailed development of ecological niche models using Maxent.


id: jbi-18270
author: Soberón, Jorge
title: Biodiversity Informatics for Public Policy. The case of CONABIO in Mexico
date: 2022
pages: 12
extension: .pdf
mime: application/pdf
words: 8151
sentence: 548
flesch: 58
cache: cache/jbi-18270.pdf
txt: txt/jbi-18270.txt
summary:
  Still, some voices have insisted that, without biodiversity data, management would be difficult or impossible (Balmford et al. 2005). What are “biodiversity data” then, how can bio- diversity data be managed in accessible ways, and what can they be used for?


id: jbi-6646
author: Mika, Katherine A.; De Veer, Joseph; Rinaldo, Constance
title: Crowdsourcing Natural History Archives: Tools for Extracting Transcriptions and Data
date: 2017
pages: 18
extension: .pdf
mime: application/pdf
words: 7821
sentence: 425
flesch: 37
cache: cache/jbi-6646.pdf
txt: txt/jbi-6646.txt
summary:
  Transcription projects for collections are time consuming, intellectually intensive, and expensive for an organization to 60 MIKA ET AL. – CROWDSOURCING NATURAL HISTORY ARCHIVES facilitate. EARLY TOOLS Two early platforms, Scripto7, developed by the Roy Rosenzweig Center for History and New Media at George Mason University (RRCHNM) and Transcribe Bentham8 shaped the landscape for successful transcription projects.


id: jbi-22444
author: Otálora-Low, Martín; Urbina-Cardona, Nicolás; González-Méndez, Mauricio
date: 2024
pages: 23
extension: .pdf
mime: application/pdf
words: 11421
sentence: 577
flesch: 53
cache: cache/jbi-22444.pdf
txt: txt/jbi-22444.txt
title:
  Enhancing Ecological Education: Utilizing Agent-Based Modeling to Simplify the Impacts of Deforestation on Amphibians

summary:
  In the model, the pasture group of species Otálora-Löw et al. – Enhancing Ecological Education 97 is represented by color Yellow, forest edge species by the blue color, and forest interior species by the green color. Classification of anuran species by forest edge response The mobile agents are the anura (frogs) and were configured based on the field abundances of the amphibian species registered by Palomino-Cuellar (2019) in 90 linear transects of 15m in length along a distance gradient from 120 m into the pastures and 400 m into the Amazon rainforest interior.


id: jbi-23641
author: Feng, Shi; Yang, Qinmin; Qiao, Huijie; Escobar, Luis E.; Yan, Xuan
title: Stopover hotspots for migratory birds in North and Central America
date: 2025
pages: 26
extension: .pdf
mime: application/pdf
words: 12059
sentence: 668
flesch: 49
cache: cache/jbi-23641.pdf
txt: txt/jbi-23641.txt
summary:
  i i icontext cell ID cell ID cell ID cell ID cell ID− − + + Based on these, the aim of this work was to investigate the stopover hotspots during the bird migration process and identify alternative stopover sites to increase the site con- nectivity along bird migratory networks.


id: jbi-23622
author: Bogoni, Juliano; Souza Campos, Derick; Muniz, Claumir; Santos-Filho, Manoel; Poletto, Jéssica
date: 2025
pages: 13
extension: .pdf
mime: application/pdf
words: 6938
sentence: 389
flesch: 45
cache: cache/jbi-23622.pdf
txt: txt/jbi-23622.txt
title:
  Welcome to the machine: A Pan-Continental overview machine learning applications in ecology and conservation

summary:
  Universal features of ecological processes exhibit mathematical properties that are inherently non-linear and complex, historically addressed only through mathemati- cal approximations (Bogoni et al., 2019; Conway, 1977; May, 1976). al. (1997), Kar et al. (2010), host-parasitoid interactions in Hassell (2000), and various other ecological dynamics, such as seed predation and dispersal (Bogoni et al., 2019) and species distribution (Bogoni and Tagliari, 2021; Tag- liari et al., 2023).


id: jbi-23179
author: Bauer, Amely; Paull, Sara; Guralnick, Robert; Campbell, Lindsay
title: Deriving best use data from NEON for mosquito research applications: A practical guide with code
date: 2025
pages: 6
extension: .pdf
mime: application/pdf
words: 4501
sentence: 185
flesch: 49
cache: cache/jbi-23179.pdf
txt: txt/jbi-23179.txt
summary:
  We also outline a set of considerations specific to filtering NEON mosquito data by sex and for day or nighttime collections, highlighting factors that could introduce uncertainty to abundance estimates. We also outline a set of considerations or “best practices” specific to filtering NEON mosquito data by sex and for day or nighttime collections and highlight additional factors that could introduce uncertainty to abun- dance estimates during trapping, sorting, and taxonomic identification.


id: jbi-23794
title: Evaluation of the knowledge gaps in the reptile records of northwestern Mexico
date: 2025
pages: 15
extension: .pdf
mime: application/pdf
words: 9556
sentence: 519
flesch: 50
cache: cache/jbi-23794.pdf
txt: txt/jbi-23794.txt
author:
  Arvizu, María Daniela; Ruiz-Luna, Arturo; Yáñez-Rivera, Beatriz; Berlanga-Robles, César Alejandro; Cuervo-Robayo, Ángela Patricia

summary:
  Number of reptile species records (RSR), number of cells with records (CWR), and number of cells by inventory complete- ness index (C) category by (a) biogeographic region (BR) and (b) physiographic province (PhP). Number of reptile species records (RSR), observed species richness (Sobs), number of species found once (a), number of spe- cies found twice (b), expected species richness (Sexp), and inventory completeness index (C) by biogeographic region, biogeographic province, and physiographic province of Nayarit.


id: jbi-9815
author: Stephens, Christopher Rhodes; Gonzalez-Salazar, Constantino; Villalobos, Maricarmen; Marquet, Pablo
title: Can Ecological Interactions be Inferred from Spatial Data?
date: 2020
pages: 44
extension: .pdf
mime: application/pdf
words: 33020
sentence: 1609
flesch: 56
cache: cache/jbi-9815.pdf
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summary:
  We can compare and contrast abiotic with biotic variables, or use different groups of biotic variables, grouped by any criterion we choose (given the data is to hand), such as by taxonomic label, or phenotype or geno- type or, by ecological interaction labels or, indeed, whatever we choose. The characterisation and quantification of ecological interactions, and the construction of species distributions and their associated ecological niches, is of fundamental theoretical and practical importance.


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id: jbi-15016
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type: ORG
entity:
  de contourner ce problème en définissant deux grandes classes de niches en fonction du type de variables utilisées pour les modéliser


id: jbi-17593
sid: 77
eid: 6
type: ORG
entity:
  compte de la possibilité de compétition entre deux espèces pour les mêmes portions de l’espace environnemental à une localité donnée


id: jbi-17593
sid: 78
eid: 3
type: WORK_OF_ART
entity:
  sein d’une même localité signifie qu’elles doivent forcément occuper des niches écologiques différentes


id: jbi-17593
sid: 111
eid: 1
type: ORG
entity:
  qui est l’expression géographique de n* f. l’intersection de gp avec m définit l’aire de distribution occupée


id: jbi-17593
sid: 132
eid: 1
type: ORG
entity:
  cela signifie que la niche fondamentale ne peut être estimée à partir de données géographiques seulement


id: jbi-17593
sid: 133
eid: 1
type: ORG
entity:
  elle doit être avant tout définie à partir de données expérimentales visant à déterminer les conditions


id: jbi-17593
sid: 162
eid: 1
type: ORG
entity:
  cela est problématique lorsque l’on cherche à transférer le modèle à une autre région ou une autre période


id: jbi-17593
sid: 189
eid: 4
type: ORG
entity:
  imprécis temporellement peut conduire à des modèles peu informatifs sur leur comportement écologique


id: jbi-17593
sid: 195
eid: 1
type: ORG
entity:
  données d’occurrences les données d’occurrences permettent de rendre compte de la répartition géographique de l’espèce ou de la


id: jbi-17593
sid: 207
eid: 1
type: ORG
entity:
  ces quelques exemples montrent que les données d’occurrences ne peuvent être interprétées simplement comme la documentation de l’absence


id: jbi-17593
sid: 214
eid: 2
type: ORG
entity:
  dans une localité en fonction des trois processus biologiques représentés dans les trois premières colonnes


id: jbi-17593
sid: 222
eid: 1
type: ORG
entity:
  les jeux d’occurrences marqués par de tels biais devront donc être employés avec des algorithmes adaptés


id: jbi-17593
sid: 227
eid: 2
type: ORG
entity:
  il est préférable de n’employer que des modèles utilisant des données de présence-seule ou de présence-background


id: jbi-17593
sid: 236
eid: 1
type: PERSON
entity:
  il est alors conseillé de recourir à un filtre environnemental en éliminant les points présentant des combinaisons de valeurs trop proches


id: jbi-17593
sid: 249
eid: 2
type: ORG
entity:
  mais il existe une infinité de cas pour lesquels mesurer l’adéquation des données à la problématique de départ est


id: jbi-17593
sid: 262
eid: 4
type: ORG
entity:
  comportent probablement des erreurs ou des incertitudes trop importantes pour être prises en compte dans une étude


id: jbi-17593
sid: 268
eid: 7
type: ORG
entity:
  leur performance dépend principalement de leur adéquation avec les données et les objectifs de l’étude


id: jbi-17593
sid: 294
eid: 1
type: FAC
entity:
  maxent va imposer des contraintes au modèle lui permettant de tenir compte des données d’occurrences tout en évitant


id: jbi-17593
sid: 295
eid: 2
type: ORG
entity:
  notamment dans l’objectif de transférer le modèle à une autre période ou une autre zone géographique


id: jbi-17593
sid: 313
eid: 1
type: ORG
entity:
  que les points de test et de calibration soient suffisamment éloignés spatialement (donc potentiellement écologiquement


id: jbi-17593
sid: 342
eid: 5
type: ORG
entity:
  la probabilité des données par rapport au modèle est calculée par le produit des scores d’adéquation des pixels contenant une présence


id: jbi-17593
sid: 402
eid: 2
type: ORG
entity:
  exemple de travaux qui cherchent à modéliser les territoires parcourus par des groupes de chasseurs-cueilleurs par le biais de la


id: jbi-17593
sid: 439
eid: 3
type: PERSON
entity:
  alors celle-ci sera probablement significative étant donné que des niches modélisées à partir de données


id: jbi-17593
sid: 445
eid: 2
type: ORG
entity:
  qui n’était employée que dans une aire géographique restreinte et des environnements relativement spécifiques


id: jbi-17593
sid: 1047
eid: 1
type: ORG
entity:
  https://cran.r-project.org/web/packages/maxnet/maxnet.pdf https://cran.r-project.org/web/packages/maxnet/maxnet.pdf anaïs vignoles


# pos

id: jbi-4019
sid: 156
tid: 4
pos: PROPN
token:
  http://www.gbif.org/communications/news-andevents/showsingle/article/gbif-beginners-guide-topersistent-identifiers-call-for-comments-on-draftdocument/.

lemma:
  http://www.gbif.org/communications/news-andevents/showsingle/article/gbif-beginners-guide-topersistent-identifiers-call-for-comments-on-draftdocument/.


id: jbi-4095
sid: 19
tid: 13
pos: SPACE
token:
                                                                                                                  

lemma:
                                                                                                                  


id: jbi-4117
sid: 266
tid: 1
pos: PROPN
token:
  http://www.gbif.org/communications/news-andevents/showsingle/article/multimedia-resourcestask-group/.

lemma:
  http://www.gbif.org/communications/news-andevents/showsingle/article/multimedia-resourcestask-group/.


id: jbi-4117
sid: 287
tid: 5
pos: NOUN
token:
  http://www.gbif.org/communications/news-and-events/showsingle/article/multimedia-resources-task-group/

lemma:
  http://www.gbif.org/communications/news-and-events/showsingle/article/multimedia-resources-task-group/


id: jbi-4126
sid: 458
tid: 3
pos: ADJ
token:
  http://www.gbif.org/communications/news-andevents/showsingle/article/gbif-content-needsassessment-survey-2009/.

lemma:
  http://www.gbif.org/communications/news-andevents/showsingle/article/gbif-content-needsassessment-survey-2009/.


id: jbi-4126
sid: 462
tid: 1
pos: PROPN
token:
  http://www.gbif.org/communications/news-andevents/showsingle/article/gbif-content-needsassessment-survey-2009-available-in-chinese/.

lemma:
  http://www.gbif.org/communications/news-andevents/showsingle/article/gbif-content-needsassessment-survey-2009-available-in-chinese/.


id: jbi-4801
sid: 34
tid: 30
pos: SPACE
token:
                                                                                                                            

lemma:
                                                                                                                            


id: jbi-4094
sid: 564
tid: 1
pos: PROPN
token:
  http://www.gbif.org/communications/news-and-events/showsingle/article/gbif-content-needs-assessment-survey-2009/

lemma:
  http://www.gbif.org/communications/news-and-events/showsingle/article/gbif-content-needs-assessment-survey-2009/


id: jbi-4094
sid: 566
tid: 2
pos: NOUN
token:
  http://www.gbif.org/communications/news-and-events/showsingle/article/gbif-content-needs-assessment-survey-2009-available-in-chinese/

lemma:
  http://www.gbif.org/communications/news-and-events/showsingle/article/gbif-content-needs-assessment-survey-2009-available-in-chinese/


id: jbi-4094
sid: 566
tid: 5
pos: PROPN
token:
  http://www.gbif.org/communications/news-and-events/showsingle/article/russkaja-versija-voprosnika-po-vyjasneniju-potrebnostei-v/

lemma:
  http://www.gbif.org/communications/news-and-events/showsingle/article/russkaja-versija-voprosnika-po-vyjasneniju-potrebnostei-v/


id: jbi-4124
sid: 63
tid: 6
pos: NOUN
token:
  http://www.gbif.org/communications/news-andevents/showsingle/article/important-quality-boost-for-gbif-data-portal/

lemma:
  http://www.gbif.org/communications/news-andevents/showsingle/article/important-quality-boost-for-gbif-data-portal/


id: jbi-6646
sid: 347
tid: 4
pos: NUM
token:
  27http://mwa2015.museumsandtheweb.com/paper/transcribing-between-the-linescrowd-sourcing-historic-data-collection/.

lemma:
  27http://mwa2015.museumsandtheweb.com/paper/transcribing-between-the-linescrowd-sourcing-historic-data-collection/.


id: jbi-6646
sid: 347
tid: 5
pos: NUM
token:
  28http://www.chronicle.com/blogs/profhacker/crowdsourcing-transcriptionfromthepage-and-scripto/38028

lemma:
  28http://www.chronicle.com/blogs/profhacker/crowdsourcing-transcriptionfromthepage-and-scripto/38028


