Biodiversity Informatics最新文献

{"title":"Completeness of Digital Accessible Knowledge of the Plants of Ghana","authors":"A. Asase, A. Peterson","doi":"10.17161/BI.V11I0.5860","DOIUrl":"https://doi.org/10.17161/BI.V11I0.5860","url":null,"abstract":"Providing comprehensive, informative, primary, research-grade biodiversity information represents an important focus of biodiversity informatics initiatives. 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. However, data on the plants of Ghana have not as yet been integrated and assessed to establish how complete site inventories are, so that appropriate levels of confidence can be applied. In this study, we assessed inventory completeness and identified gaps in current Digital Accessible Knowledge (DAK) of the plants of Ghana, to prioritize areas for future surveys and inventories. We evaluated the completeness of inventories at ½° spatial resolution using statistics that summarize inventory completeness, and characterized gaps in coverage in terms of geographic distance and climatic difference from well-documented sites across the country. The southwestern and southeastern parts of the country held many well-known grid cells; the largest spatial gaps were found in central and northern parts of the country. Climatic difference showed contrasting patterns, with a dramatic gap in coverage in central-northern Ghana. This study provides a detailed case study of how to prioritize for new botanical surveys and inventories based on existing DAK.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"24 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126336624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biodiversity Informatics Training Curriculum, version 1.2","authors":"Eric B. Fokam, L. Krishtalka","doi":"10.17161/BI.V11I0.5008","DOIUrl":"https://doi.org/10.17161/BI.V11I0.5008","url":null,"abstract":"The Biodiversity Informatics Training Curriculum represents an integration of three years of teaching and interaction by many instructors and students in a series of interactions in courses across Africa. Digital videos of these courses--shared openly via YouTube--have been compiled into a first field-wide curriculum, which is presented herein. The compilation is, in effect, a digital textbook covering the entire field of biodiversity informatics.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"36 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129399489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"THE PRESENT STATE OF BOTANICAL INVESTIGATIONS IN CÔTE D’IVOIRE","authors":"K. J. Koffi, Akossoua Faustine Kouassi, C. Y. A. Yao, A. Bakayoko, I. J. Ipou, J. Bogaert","doi":"10.17161/bi.v10i2.5007","DOIUrl":"https://doi.org/10.17161/bi.v10i2.5007","url":null,"abstract":"The aim of this present study is to summarize the current state of research on the flora of the Cote d’Ivoire from the SIG IVOIRE database to better direct future collection efforts. Herbarium specimen data used for this study covered the period from 1894 to 2000, and were assembled by 226 collectors. This database comprises 15,228 samples, grouped in 3621 species, 1371 genera, and 198 families. A grid system was used to cover the Ivorian territory at spatial resolution of 0.75° x 0.75°. Indices of evenness and completeness were calculated to characterize sampling and identify floristically well-known regions. The exploration of the Ivorian territory is far from uniform, such that some areas were more densely surveyed, but others partially or not at all. The regions of Grands Ponts, Agneby-Tiassa, Loh-Djiboua, part of Gbeke, Boukani, San Pedro and Cavally were floristically well known; environmentally, the largest gaps in coverge were in the mountains in western Cote d'Ivoire.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"64 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131518416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"INDICES OF BIODIVERSITY PATTERN BASED ON PRESENCE-ABSENCE MATRICES: A GIS IMPLEMENTATION","authors":"Jorge Soberón, J. Cavner","doi":"10.17161/BI.V10I0.4801","DOIUrl":"https://doi.org/10.17161/BI.V10I0.4801","url":null,"abstract":"In this work we present mathematical notation and formulae relating a number of indices of the biodiversity pattern of an aggregate of species, and an Open Source implementation of them as a plug-in for the increasingly popular Open Source geographical information system Quantum GIS. We provide detailed formulae relating three indices of beta diversity, two of pattern of nestedness, one of checkerboard pattern, and two of ratios of variances. The above is done by deriving six vectors from the full presence-absence matrix. Our GIS implementation is done via Web Services, tapping the LifeMapper platform for calculating potential species distributions.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"10 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132972730","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"OMWS: A Web Service Interface for Ecological Niche Modelling","authors":"R. Giovanni, E. Torres, Rafael Amaral, I. Blanquer, Vinod E. F. Rebello, V. Canhos","doi":"10.17161/BI.V10I0.4853","DOIUrl":"https://doi.org/10.17161/BI.V10I0.4853","url":null,"abstract":"Ecological niche modelling (ENM) experiments often involve a high number of tasks to be performed. Such tasks may consume a significant amount of computing resources and take a long time to complete, especially when using personal computers. OMWS is a Web service interface that allows more powerful computing back-ends to be remotely exploited by other applications to carry out ENM tasks. Its latest version includes a new operation that can be used to specify complex workflows in a single request, adding the possibility of using workflow management systems on parallel computing back-end. In this paper we describe the OMWS protocol and compare its most recent version with the previous one by running the same ENM experiment using two functionally equivalent clients, each designed for one of the OMWS interface versions. Different back-end configurations were used to investigate how the performance scales for each protocol version when more processing power is made available. Results show that the new version outperforms (in a factor of 2) the previous one when more computing resources are used.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"85 2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123067830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"EcoClimate: a database of climate data from multiple models for past, present, and future for macroecologists and biogeographers","authors":"M. Lima-Ribeiro, Sara Varela, J. González-Hernández, G. Oliveira, J. Diniz‐Filho, L. C. Terribile","doi":"10.17161/BI.V10I0.4955","DOIUrl":"https://doi.org/10.17161/BI.V10I0.4955","url":null,"abstract":"Studies in biogeography and macroecology have been increasing massively since climate and biodiversity databases became easily accessible. Climate simulations for past, present, and future have enabled macroecologists and biogeographers to combine data on species' occurrences with detailed information on climatic conditions through time to predict biological responses across large spatial and temporal scales. Here we present and describe ecoClimate, a free and open data repository developed to serve useful climate data to macroecologists and biogeographers. ecoClimate arose from the need for climate layers with which to build ecological niche models and test macroecological and biogeographic hypotheses in the past, present, and future. ecoClimate offers a suite of processed, multi-temporal climate data sets from the most recent multi-model ensembles developed by the Coupled Modeling Intercomparison Projects (CMIP5) and Paleoclimate Modeling Intercomparison Projects (PMIP3) across past, present, and future time frames, at global extents and 0.5° spatial resolution, in convenient formats for analysis and manipulation. A priority of ecoClimate is consistency across these diverse data, but retaining information on uncertainties among model predictions. The ecoClimate research group intends to maintain the web repository updated continuously as new model outputs become available, as well as software that makes our workflows broadly accessible.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"96 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128777095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DIVERSITY OF WILD PALMS (ARECACEAE) IN THE REPUBLIC OF BENIN: FINDING THE GAPS IN THE NATIONAL INVENTORY COMBINING FIELD AND DIGITAL ACCESSIBLE KNOWLEDGE","authors":"R. Idohou, Arturo H. Ariño, A. Assogbadjo, R. G. Kakaï, B. Sinsin","doi":"10.17161/BI.V10I2.4914","DOIUrl":"https://doi.org/10.17161/BI.V10I2.4914","url":null,"abstract":"Despite many efforts by researchers worldwide to assess the biodiversity of plant groups, many locations on Earth remain not well surveyed and data-deprivation biases often occur. Robust estimates of inventory completeness could help alleviate the problem. This study aimed at identifying areas representing gaps in current knowledge of African palms, with a focus on Benin (West Africa). We assessed the completeness of knowledge of African palms targeting geographical distance and climatic difference from well-known sites. Data derived from intensive fieldwork were combined with independent data available online. Completeness inventory indices were calculated and coupled with other criteria to decide on the extent of knowledge. Results showed a high overall value for inventory completeness, as well as an even distribution of well-known areas across the country. However, poorly-known areas were distinctly identified and correlated to remote locations with low accessibility. This study illustrates how biodiversity survey and inventory efforts can be guided by existing knowledge. We strongly recommend the combination of digital accessible knowledge and fieldwork, coupled with expert knowledge, to obtain a better picture of the completeness of the inventory in tropical ecosystems.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"18 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116519736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Digital Knowledge of Kenyan Succulent Flora and Priorities for Future Inventory and Documentation","authors":"E. Wabuyele, S. Kang’ethe, L. Newton","doi":"10.17161/BI.V11I0.4959","DOIUrl":"https://doi.org/10.17161/BI.V11I0.4959","url":null,"abstract":"Biodiversity inventory in Kenya has been ongoing for about a century and a half, coinciding with the arrival of naturalists from Europe, America, and elsewhere outside Africa. Since the first collections in the mid-to-late 1800s, there has been a steady increase of plant surveys, frequency of inventory, and discovery of new species that have considerably increased knowledge of faunal and floristic elements. However, as in all other countries, such historical biological collection activities are more often than not, ad hoc, resulting in gaps in knowledge of species and their habitats. While Kenya is relatively rich botanically, with a succulent flora of about 428 taxa, it is apparent that the list is understated owing to, among other factors, difficulty of preparing herbarium material and restricted access to some sites. This study investigated completeness of geographic knowledge of succulent plants in Kenya, with the aim of establishing species distribution patterns and identifying gaps that will guide and justify priority setting for future work on the group. Species data were filtered from the general BRAHMS database at the East African Herbarium and cleaned via an iterative series of inspections and visualizations designed to detect and document inconsistencies in taxonomic concepts, geographic coordinates, and dates of collection. Eight grid squares fulfilled criteria for completeness of inventory: one in the city of Mombasa, one in the Kulal–Nyiro complex, one in Garissa, one in Baringo, and four grid squares in the Nairobi–Nakuru–Laikipia area. Poorly-known areas, mostly in the west, north, and north-eastern regions of the country, were extremely isolated from well-known sites, both geographically and environmentally. These localities should be prioritised for future inventory as they are likely to yield species new to science, species new to the national flora, and/or contribute new knowledge on habitats. To avoid inconsistencies and data leakage, biodiversity inventory and documentation needs streamlining to generate standardised metadata that should be digitised to enhance access and synthesis.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131287293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DigiWeb - a workflow environment for quality assurance of transcription in digitization of natural history collections","authors":"T. Mononen, Riitta Tegelberg, M. Sääskilahti, Markku A. Huttunen, Marko Tähtinen, H. Saarenmaa","doi":"10.17161/BI.V9I1.4748","DOIUrl":"https://doi.org/10.17161/BI.V9I1.4748","url":null,"abstract":"Data produced by digitization increases the scientific use of natural history collections. However, in mass digitization, attention must be paid to the flawless management of the workflows, and high quantities of end results should not be compromised by a low standard of quality. A web-based environment DigiWeb was created for controlling the workflow of transcribing data from images of natural history specimens. Using DigiWeb , it was possible to manage the workflow of transcription and data proofing, include all participants to the workflow, allow collaboration and training, and also to provide useful processing features. The data emerging from this process passes quality control standards which are supported by DigiWeb and based on the strict requirements of the ISO 2859 standard.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"71 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127352311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PointSampler: A GIS Tool for Point Intercept Sampling of Digital Images","authors":"D. Gobbett, A. Zerger","doi":"10.17161/BI.V9I1.4717","DOIUrl":"https://doi.org/10.17161/BI.V9I1.4717","url":null,"abstract":"Close-range digital photography to assess vegetation cover is useful in disciplines ranging from ecological monitoring to agricultural research. An on-screen point intercept sampling method, which is analogous to the equivalent field based method, can be used to manually derive the percentage occurrence of multiple cover classes within an image. PointSampler is a GIS embedded tool that provides a semi-automated approach for performing point intercept sampling of digital images, and which integrates with existing GIS functionality and workflows. We describe and illustrate the two general applications of this tool, in in efficiently deriving primary ecological data from digital photographs , and for the generation of validation data to complement automated image classification of a time series of groundcover images.  The flexible design and GIS integration of PointSampler allows it to be put to a wide range of similar uses.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"28 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129357942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}