Data accessed through the FBIS are free for all—but not free of obligations. Under the terms of the FBIS data users agreement, users who download individual datasets or search results and use them in research or policy agree to cite them using the referencing information provided in the metadata for each data record.
+Good citation practices ensure scientific transparency and reproducibility by guiding other researchers to the original sources of information. They also reward data-publishing institutions and individuals by reinforcing the value of sharing open data and demonstrating its impact to their stakeholders and funders.
+Users are strongly encouraged to cite data retrieved from the FBIS network according to the recommended citation:
+Freshwater Biodiversity Information System (FBIS). 2022. Downloaded from https://freshwaterbiodiversity.org on [current date]
+++Note: Users also need to cite the individual source references that they have used, which are available in the metadata table provided on the detailed dashboards.
+
To cite the scientific article published in the African Journal of Aquatic Science.
+Dallas HF, Shelton JM, Sutton T, Tri Ciputra D, Kajee M and Job N. 2021. Development of a freshwater biodiversity information system for evaluating long-term change in rivers in South Africa. African Journal of Aquatic Science. doi.org/10.2989/16085914.2021.1982672
+To cite the User Manual:
+Freshwater Biodiversity Information System (FBIS). 2022. FBIS User Manual. Prepared by the Freshwater Research Centre and Kartoza.
+Website:
+ +
Kajee Mohammed, Henry Dominic A. W., Dallas Helen F., Griffiths Charles L., Pegg Josephine, Van der Colff Dewidine, Impson Dean, Chakona Albert, Raimondo Domitilla C., Job Nancy M., Paxton Bruce R., Jordaan Martine S., Bills Roger, Roux Francois, Zengeya Tsungai A., Hoffman Andre, Rivers-Moore Nick, Shelton Jeremy M. (2023) How the Freshwater Biodiversity Information System (FBIS) is supporting national freshwater fish conservation decisions in South Africa, Frontiers in Environmental Science, Vol 11, DOI: DOI=10.3389/fenvs.2023.1122223
+https://www.frontiersin.org/articles/10.3389/fenvs.2023.1122223
+Helen Dallas, Jeremy Shelton, Tim Sutton, Dimas Tri Cuptura, Mohammed Kajee & Nancy Job (2022) The Freshwater Biodiversity Information System (FBIS) – mobilising data for evaluating long-term change in South African rivers, African Journal of Aquatic Science, 47:3, 291-306, DOI: 10.2989/16085914.2021.1982672
+https://www.tandfonline.com/doi/abs/10.2989/16085914.2021.1982672
+Kajee, Mohammed, Helen F. Dallas, Aneri Swanepoel, Charles L. Griffiths, and Jeremy M. Shelton. 2023. “The Freshwater Biodiversity Information System (FBIS) Fish Data: A Georeferenced Dataset of Freshwater Fishes Occurring in South Africa”. Journal of Limnology 82 (s1).
+https://doi.org/10.4081/jlimnol.2023.2133.
+The past and current distribution of native and non-native fish in the Kowie River catchment, Makhanda, Eastern Cape +Dumisani Khosa, Josie South, Ncumisa Y. Matam, Lubabalo Mofu, Ryan J. Wasserman and Olaf L.F. Weyl +Knowl. Manag. Aquat. Ecosyst., 424 (2023) 3
+https://doi.org/10.1051/kmae/2022026
+Helen Dallas, Jeremy Shelton, Tim Sutton, Dimas Tri Ciptura, Mohammed Kajee & Nancy Job (2022) The Freshwater Biodiversity Information System (FBIS) – mobilising data for evaluating long-term change in South African rivers. African Journal of Aquatic Science, 47:3, 291-306, DOI: 10.2989/16085914.2021.1982672 +https://www.tandfonline.com/
+Kajee Mohammed, Henry Dominic A. W., Dallas Helen F., Griffiths Charles L., Pegg Josephine, Van der Colff Dewidine, Impson Dean, Chakona Albert, Raimondo Domitilla C., Job Nancy M., Paxton Bruce R., Jordaan Martine S., Bills Roger, Roux Francois, Zengeya Tsungai A., Hoffman Andre, Rivers-Moore Nick, Shelton Jeremy M. (2023) How the Freshwater Biodiversity Information System (FBIS) is supporting national freshwater fish conservation decisions in South Africa. Frontiers in Environmental Science, Vol 11, DOI: DOI=10.3389/fenvs.2023.1122223 +https://www.frontiersin.org/
+Kajee, Mohammed, Helen F. Dallas, Aneri Swanepoel, Charles L. Griffiths, and Jeremy M. Shelton. 2023. The Freshwater Biodiversity Information System (FBIS) Fish Data: A Georeferenced Dataset of Freshwater Fishes Occurring in South Africa. Journal of Limnology 82 (s1). +https://doi.org/10.4081/
+Dumisani Khosa, Josie South, Ncumisa Y. Matam, Lubabalo Mofu, Ryan J. Wasserman and Olaf L.F. Weyl. The past and current distribution of native and non-native fish in the Kowie River catchment, Makhanda, Eastern Cape. Knowl. Manag. Aquat. Ecosyst., 424 (2023) 3 +https://doi.org/10.1051/kmae/
+Céline C. Hanzen, Martyn C. Lucas, Olaf L.F. Weyl, Sean M. Marr, Gordon O’Brien, Colleen T. Downs (2022). Slippery customers for conservation: Distribution and decline of anguillid eels in South Africa. Volume32, Issue 8, Pages 1277-1290. https://doi.org/10.1002/aqc.
+Mahomed Desai, Celine Hanzen, Colleen T. Downs, Gordon C. O’Brien (2021) Environmental drivers of ichthyofauna community composition of the river ecosystems draining the Lake St. Lucia basin, South Africa. Hydrobiologia 848:3539–3554 +https://doi.org/10.1007/
+Toni Belcher (2022) Aquatic Biodiversity Impact Assessment: Farm 1441, Jonkershoek, Stellenbosch in the Western Cape.
+Dallas HF, Shelton JM, Sutton T, Tri Ciputra D, Kajee M and Job N. 2022. The Freshwater Biodiversity Information System (FBIS) – mobilising data for evaluating long-term change in South African rivers, African Journal of Aquatic Science 47(3): 291-306, DOI: 10.2989/16085914.2021.1982672
+Desai M, Hanzen C, Downs CT, O’Brien GC. 2021. Environmental drivers of ichthyofauna community composition of the river ecosystems draining the Lake St. Lucia basin, South Africa. Hydrobiologia 848:3539–3554 +https://doi.org/10.1007/s10750-021-04609-7
+Khosa D, South J, Matam NY, Mofu L, Wasserman RJ and Weyl OLF. 2023. The past and current distribution of native and non-native fish in the Kowie River catchment, Makhanda, Eastern Cape. Knowl. Manag. Aquat. Ecosyst., 424. DOI: https://doi.org/10.1051/kmae/2022026
+Hanzen CC, Lucas MC, Weyl OLF, Marr SM, O’Brien G and Downs CT. 2022. Slippery customers for conservation: Distribution and decline of anguillid eels in South Africa. Aquatic Conservation: Marine and Freshwater Ecosystems, 32: 1277– 1290. https://doi.org/10.1002/aqc.3823
+Kajee M, Henry DAW, Dallas HF, Griffiths CL, Pegg J, Ven der Coll D, Impson D, Chakona A, Raimondo DC, Job NM, Paxton BR, Jordaan MS, Bills R, Roux F, Zengeya TA, Hoffman A, Rivers-Moore N, Shelton JM. 2023. How the Freshwater Biodiversity Information System (FBIS) is supporting national freshwater fish conservation decisions in South Africa. Frontiers in Environmental Science. Vol 11, +https://www.frontiersin.org/articles/10.3389/fenvs.2023.1122223
+Kajee M, Dallas HF, Swanepoel A, Griffiths CL, and Shelton JM. 2023. The Freshwater Biodiversity Information System (FBIS) Fish Data: A Georeferenced Dataset of Freshwater Fishes Occurring in South Africa. Journal of Limnology 82 (s1). https://doi.org/10.4081/jlimnol.2023.2133
+King J and Palmer C. 2022. Perspectives on Protecting African freshwater Ecosystems in the Anthropocene. African Journal of Aquatic Science. 47(3): iii-vi.
+The Department of Forestry Fisheries and Environment (DFFE) National Environmental Screening Tool Aquatic Biodiversity Sensitivity Layers. 2023.
+Shelton J, Jordaan M, Dallas H, van der Colff D, Kajee M, Impson D, Henry D, Khosa D, Raimondo D, Job N, Chakona A. 2023. The Department of Forestry Fisheries and Environment (DFFE) Environmental Assessment Protocols: Freshwater fish fauna.
+GEO BON and FWBON, 2022. Inland Waters in the Post-2020 Global Biodiversity Framework. Available from https://geobon.org/science-briefs/.
+Day JA and BR Davies. 2022. Vanishing Waters (3rd ed.) Water research Commission Special Report SR 160/22, Water Research Commission, Pretoria, South Africa.
+Fry C. 2021. A field guide to freshwater macroinvertebrates of southern Africa. Jacana Press. South Africa.
+Machingura J, Coetzee J, Dallas H, Day B, Day J, Hay D, Skelton P, Thirion C and Uys M. 2021. The evolution of ecosystem research – from biodiversity to biossessments. Chapter 7 In: WRC@50: Celebrating a half century of excellence (Eds. Day JA, Day B and Reizenberg J). Water Research Commission Report no. SP 148/21, Water Research Commission, Pretoria, South Africa.
+Turak E, Van Deventer H, Pienaar M, Walters M, Dallas H, etc. In prep. Collection and management of biological records must support protection and restoration goals for freshwater species and ecosystems.
+++Note: Numerous consultants use the data from FBIS is their reports. Not all correctly cite the FBIS yet.
+
CapeNature 2022. Field Report 4/2022. Jonkershoek Nature Reserve Eerste River winter monitoring report. Unpublished internal report. Field report. CapeNature 2022. Field Report 10/2022. Jonkershoek Nature Reserve Eerste River autumn monitoring report. Unpublished internal report. Field report.
+Toni Belcher (2022) Aquatic Biodiversity Impact Assessment: Farm 1441, Jonkershoek, Stellenbosch in the Western Cape.
+CapeNature, 30/03/2022, Field Report: River survey of the Outeniqua Nature Reserve Complex, Unpublished internal report, Biodiversity Capabilities: Technical Report.
+CapeNature 2023. Field Report 2/2023. Kogelberg Nature Reserve annual SASS monitoring report. Unpublished internal report. Field report.
+City of Cape Town. In prep. Hout Bay River – State of the Rivers report. Scientific Services. City of Cape Town.
+Erasmus P. 2022. Basic Assessment Report For The Proposed Prospecting Activities On Various Farms, In The Magisterial District Of Blouberg And Mogalakwena, Limpopo Province For Sylvania Northern Mining (Pty) Ltd For the following Minerals: Chrome Ore, Cobalt, Copper Ore, Gold Ore, Nickel Ore, Platinum Group Metals Located on the Farms: Altona 696 LR, Gillemberg 861 LR, Non Plus Ultra 683 LR, Teneriffe 682 LR, Aurora 397 LR and Nonnenwerth 421 LR, in the Magisterial Districts of there Blouberg and Mogalakwena, Limpopo Province DMRE Reference Number: LP30/5/1/1/2/14710PR. Prescali Environmental Consultants (Pty) Ltd. Pretoria
+Erasmus P. 2022. Basic Assessment Report For The Proposed Prospecting Activities On Various Farms, In The Magisterial District Of Blouberg And Mogalakwena, Limpopo Province For Sylvania Northern Mining (Pty) Ltd For the following Minerals: Chrome Ore, Cobalt, Copper Ore, Gold Ore, Nickel Ore, Platinum Group Metals Located on the Farm: Portion 2 of the Farm Schaffhausen 689 LR, in the Magisterial District of Blouberg, Limpopo Province DMRE Reference Number: LP30/5/1/1/2/14728PR. Prescali Environmental Consultants (Pty) Ltd. Pretoria
+Erasmus P. 2023. Desktop Surface Water Assessment Report for Kegakilwe Trading (Pty) Ltd - situated on Portion 0 of the Farm Mooikloof 150 and Portion 5 of the Farm Oatlands 151 within the Waterberg District in the Limpopo Province. Prescali Environmental Consultants (Pty) Ltd. Pretoria.
+Erasmus P. 2022. Desktop Surface Water Assessment Report for Maditse Investments - situated on the Farms Tabana 133 LR, Boekenhoutfontein 108 LR and Prairie 107 LR within the Waterberg District in the Limpopo Province. Prescali Environmental Consultants (Pty) Ltd. Pretoria.
+Erasmus P. 2022. Surface Water Assessment Report for Mofenyi Mining - Modjadji situated on Modjadji No. 1 934-LT within the Mopanie District in the Limpopo Province. Prescali Environmental Consultants (Pty) Ltd. Pretoria.
+Erasmus P. 2022. Desktop Surface Water Assessment Report for Regison Mining (Pty) Ltd - situated on the Farms Greater Giyani 891 LT and Mariyeta 246 LT within the Mopani District in the Limpopo Province. Prescali Environmental Consultants (Pty) Ltd. Pretoria.
+Fry, C. 2022. A field guide to freshwater macroinvertebrates in southern Africa. Jacana Media. South Africa.
+Quale L. 2020. State of Strategic Water Source Areas Monitoring and Reporting Framework, and Information Platform – Southern Drakensberg Pilot. Institute for Natural Resources, South Africa.
+Rivers-Moore NA and Kajee M. 2020. Pilot study on the use of the Freshwater Biodiversity Information System (FBIS) as a tool to extract data for climate change impacts on aquatic species distribution models. Freshwater Research Centre, Cape Town, South Africa.
+Kajee. M. In prep. Trajectories of change is South Africa’s freshwater fish fauna. PhD Thesis. University of Cape Town.
+Dallas HF and Rivers-Moore NA. 2019. Environmental water temperature guidelines for perennial rivers: A protocol and tools for setting water temperature targets in South Africa. Southern African Society for Southern Africa Conference, Limpopo July 2019.
+Dallas HF and Shelton JM. 2017. Building freshwater information systems to last: A freshwater biodiversity information system for evaluating long‐term change in rivers in the Cape Floristic Region, South Africa. JRS Biodiversity Symposium, Johannesburg, South Africa.
+Dallas HF, Shelton J, Olsen T, Sutton T and Ciputra D. 2019. Developing a freshwater biodiversity information system for evaluating long-term change in South African rivers. Southern African Society for Southern Africa Conference, Limpopo July 2019.
+Dallas HF, Shelton J, Sutton T, Tri Cuptura D, Kajee M, Job N. 2021. The Freshwater Biodiversity Information System (FBIS) – a user-driven information system for mobilising, visualising and reporting biodiversity data in South Africa. Southern African Society for Southern Africa Conference, Virtual conference November 2021.
+Dallas HF, Shelton J, Sutton T, Tri Cuptura D, Kajee M, Job N. 2021. Biodiversity data at your fingertips: the Freshwater Biodiversity Information System (FBIS). National Wetlands Indaba, Virtual conference October 2021.
+Dallas HF. 2019. User driven information system design – more carrot less stick. JRS Biodiversity Symposium, Nairobi, Kenya.
+Dallas HF. 2022. Biodiversity data at your fingertips: the Freshwater Biodiversity Information System (FBIS). Keynote Address at the Biodiversity Information Conference. November 2022.
+Kajee M, Dallas HF, Shelton JM and Griffiths CL. 2019. Consolidating data on the status, distribution and abundance of South African freshwater fishes, invertebrates and algae for incorporating into a Freshwater Biodiversity Information System (FBIS) and assessing long-term change. South African National Biodiversity Institute Biodiversity Planning Forum, 4–7 June, Northern Drakensburg.
+Kajee M, Dallas HF, Shelton JM and Griffiths CL. 2019. The status of South African freshwater fishes: A prelude to predicting the impacts of climate change on selected South African freshwater fish. Department of Biological Sciences Careers and Research Day, 21 November, Cape Town.
+Kajee M, Dallas HF, Shelton JM and Griffiths CL. 2019. The status of South African freshwater fishes: A prelude to predicting the impacts of climate change on selected South African freshwater fish. +12th SAEON Graduate Student Network Indibano, 1–6 September, Cape St Francis (Best student presentation).
+Kajee M, Dallas HF, Shelton JM and Griffiths CL. 2019. The status, distribution and abundance of South African freshwater fishes: A prelude to predicting the impacts of climate change on selected South African freshwater fish. 39th Zoological Society of Southern Africa (ZSSA) Congress, 7–10 July, Skukuza, Kruger National Park.
+Kajee M, Dallas HF, Shelton JM and Griffiths CL. 2020. The status of South African freshwater fishes: A prelude to predicting the impacts of climate change on selected South African freshwater fish. W12 Congress: 1st International Meeting of Cities Tackling Water Challenges, 27-28 November, Cape Town.
+Kajee M, Dallas HF, Shelton JM and Griffiths CL. 2021. South African fish data in FBIS: A success story. Southern African Society of Aquatic Scientists Congress, 1-3 November, Virtual Event. +Kajee M, Dallas HF, Shelton JM and Griffiths CL. 2021. South African fish data in FBIS: A success story. National Wetlands Indaba 2021, 20-21 October, Virtual Event (Best student presentation).
+Kajee, M., Dallas, H.F., Shelton JM and Griffiths CL. 2022. South African National Biodiversity Institute 4th Annual Student Research Day, 29-30 March, Cape Town.
+Shelton J and Dallas HF. 2021. Mobilising freshwater biodiversity data for South African rivers – successes, challenges, data providers, future expansion Southern African Society for Southern Africa Conference, Virtual conference November 2021.
+Shelton J and Dallas HF. 2022. How the Freshwater Biodiversity Information System (FBIS) is supporting freshwater fish conservation in South Africa. Biodiversity Information Conference. November 2022.
+Shelton J, Dallas HF, Kajee M. The Freshwater Biodiversity Information System (FBIS): +Unlocking data for improved freshwater decision-making in South Africa. Berg River Improvement Programme. Jonkershoek. June 2023.
+Shelton J and Dallas HF. 2023. The Freshwater Biodiversity Information System (FBIS): +Unlocking data for improved freshwater decision-making in South Africa. City of Cape Town, Athlone Sewage works. August 2023.
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This project is open source, so you can create a pull request(PR) after you fix issues. Get a local copy of the plugins checked out for development using the following process.
+Before uploading your PR, run test one last time to check if there are any errors. If it has no errors, commit and then push it!
+For more information on PR's steps, please see links in the Contributing section.
+Please make this project more fun and easy to scan by using emoji prefixes for your +commit messages (see GitMoji).
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Web Site: https://freshwaterbiodiversity.org/
+The Freshwater Biodiversity Information System (FBIS), South Africa.
+
The FBIS serves as a community platform for inventory and maintenance of freshwater biodiversity data with an end goal to assist the evaluation of long-term change in river biodiversity and ecosystem condition in South Africa.
+This project is funded by the JRS Biodiversity Foundation and SANBI, and implemented by the FRC and Kartoza.
+By signing up and creating an account you will be able to (1) explore the map, (2) query the data in the system, (3) download maps, data, graphs and reports and (4) create a site and upload data. If you do not sign up, you will still have access to all the above functions except the ability to upload data.
+The FBIS v3 release includes access to FBIS, a FBIS v3 user manual (accessed via the 'Help' tab on the top bar of the site) and a short ‘how to’ video series available here.
+These aids should help you to navigate your way around the system and test out the main functions, features and work flows, as well as flag any issues you pick up on while testing.
+Any questions can be directed to fbis@frcsa.org.za.
+We look forward to receiving your feedback!
Examples of running instances of the Biodiversity Information Management System (BIMS) are:
+
Web Site: https://orbis.kartoza.com
+The Okavango Repository for BiodiverSity Data (ORBIS), Botswana
+
The Okavango Repository for BIodiverSity Data (ORBIS) is conceptualised to bridge the gap between biodiversity data collectors and users in Botswana, with an emphasis on policymakers responsible for conservation management decisions.
+Through continued engagement with stakeholders via the ORBIS reference group and capacity-building activities, ORBIS will improve the pathways from biodiversity data to policies, ensuring that stakeholders are empowered to make evidence-based decisions relating to biodiversity management.
+For more information, contact us at: ebennitt@ub.ac.bw
Web Site: https://rbis.ur.ac.rw/
+We are CoEB - the Center of Excellence in Biodiversity and Natural Resource Management, Rwanda
+
CoEB is a Rwandan Government institution that functions as a consortium of governmental and non-governmental organizations, bringing together expertise and skills to produce information needed for effective policy and science-driven economic transformation. The Center is hosted at University of Rwanda and works in three areas: research and monitoring, bioprospecting, and conservation education and awareness raising.
+The Center plays a catalytic and coordinating role to ensure sharing of scientific knowledge and expertise for evidence-based decisions in conservation, natural resource management and climate resiliency. We provide leadership, best practices, research, support and training in the domain of biodiversity, natural resource management, and impacts of climate change on ecosystems and livelihoods. The goal is to encourage, enable and support stakeholders to generate and apply knowledge on biodiversity and natural resources for sustainable development. We address the need for data for national reporting requirements (CBD, NDC, etc.) and to inform existing indicators of global biodiversity trends, such as the Living Planet Index from WWF, the Red List Index, GEO BON Species Protection Index, and the need for data in land use planning decisions, restoration projects, and ecosystem health and services provisioning.
+A biodiversity information system takes biodiversity observation records that are stored in a variety of sources and formats and puts them into a standardized format on a viewing platform to enable stakeholders to access and use the information. Biodiversity data for Rwanda have been scattered and difficult to access, but are critical to understanding patterns of biodiversity distribution, ecosystem functioning, and early detection of environmental change. Species records can provide indication of climate change impacts, pollution effects, and guide development, land use planning, tourism opportunities, and monitoring of restoration efforts. An information system puts data at your fingertips for national reporting requirement needs like the CBD and NDC. The system effectively links research to conservation and policy.
+With funding from the JRS Biodiversity Foundation https://jrsbiodiversity.org/ we are developing the first national biodiversity information system for Rwanda. We call it the Rwanda Biodiversity Information System or RBIS. Thanks to generous collaboration from data holders who graciously shared their data sets, including independent researchers, NGOs and government institutions, we have already mobilized more than 30,000 biodiversity data records.
+We begin the RBIS with a focus on biodiversity data in freshwater ecosystems. We have mobilized data on odonates, anurans, and birds, thanks to the generous data sharing by data holders. Our aim is to demonstrate the power of the RBIS to inform wetlands and catchment management using biodiversity data to indicate ecosystem health. We will eventually scale the RBIS up to include all ecosystems in Rwanda.
+When you enter the Explore button, you will see the base map of Rwanda and you can begin to explore and query the system for information. We hope you find this resource valuable and we welcome your feedback.
+For more information, contact us at: coeb1@ur.ac.rw
Data management guide for the Freshwater Biodiversity Information System (FBIS): a platform for housing and serving freshwater biodiversity data.
+These documents serves as a guideline for the management of freshwater biodiversity data in the Freshwater Biodiversity Information System (FBIS). It provides an overview of the recommended steps, processes and systems for sourcing, extracting, consolidating, uploading and serving biodiversity data in an information system such as FBIS. It is based on the experiences gained and systems developed during the development of the Freshwater Biodiversity Information System (FBIS) in South Africa (Freshwater Biodiversity Information System. 2020. FBIS Version 3; Dallas et al. 2022).
+Establishing what data are available in a country is the first step in the data process. To assist with the managing of data we recommend developing a DataSet Tracker.
+Often the amount of data available for consolidation into an information system, exceeds the amount of data that can actually be consolidated based on time and financial constraints. It is thus critical that the FBIS data team prioritise the data for FBIS. This is best done through consultation with the end-users and stakeholders of FBIS. To manage the prioritisation of data and keep track of progress, a DataSet Tracker is used. This is an excel spreadsheet that keeps track of the data available for inclusion in FBIS, and importantly allows for prioritisation of each data set into FBIS.
+The DataSet Tracker provides a list and details of data sets identified by the FBIS team and stakeholders, which are being considered for inclusion in the FBIS. Data are best divided into four broad categories, namely:
+For each category, the FBIS team needs to specify the following:
+A DataSet Tracker template has been generated for FBIS (FBIS DataSet Tracker Template.xlsx). For spatial data it is important to indicate if this layer is to be used as a filter, spatial layer, or both (see details in 32.3.3 Spatial Data).
+Data sourcing, extraction and consolidation requires careful, accurate and concise work to ensure quality data. A robust system for managing the data consolidation process is recommended. Github is an excellent tool for managing this process as it allows multiple team members to work together in one project, which allows for easy management of workflows for data consolidation. A screenshot of the FBIS Data Management project on GitHub is provided (Figure 1). Using GitHub one can:
+The FBIS will be introduced to GitHub for managing both the technical and data side of the FBIS project.
+Figure 1. Example of data management workflow in GitHub
+
Biodiversity data is the primary currency of FBIS. The lowest unit is an occurrence record for a Taxon taken at a Site (identified by a latitude / longitude) on a particular Sampling Date (so Taxon, location and date – these are mandatory attributes for each record). For some taxa extra attributes may be included such as habitat or biotope. Additional data may be associated with each occurrence record, although this is often dependent on the group (birds, fish, invertebrates, wetland plants, algae) being focused on, and may vary somewhat from one group to another. For each occurrence record, Presence = 1 indicates that the species was recorded at a site on a particular sampling date. In addition, we have included the option to include sampling method, sampling effort, abundance measure, and abundance for each; as well as a number of abiotic parameters associated with each occurrence record (see 32.3.2 Abiotic data). Further details are provided in 32.4.2 Data Upload Templates.
+A taxonomic Master List is a list of all species and/or taxa within a particular group such as birds, fish, invertebrates, wetland plants, algae, etc. For some groups a species list is easy to produce as species level is commonly identified in studies (e.g. birds, fish). For other groups, the taxonomic level (family, genus, species etc) varies considerably from study to study, and thus it is recommended that the lowest taxonomic level is used and that Taxon is used in preference to Species (e.g. invertebrates, algae).
+The purpose of the Master List is threefold:
+The generation of a Master List requires consultation with available resources, relevant publications and experts. A Master List is intended to be an updatable resource, improved and added to as new data and studies are published, or new taxa are described. If no species lists are available for a country then the GBIF Taxonomic Master List may be generated by extracting data from GBIF. This Master List should then ideally be checked and validated for accuracy by the FBIS team.
+The format of the Master List is important to ensure consistency for ingestion of data into the information system. The following columns are included in the Master Lists, provided as excel file template that will be used for each FBIS group (Master List Template final for FBIS Generic 2022_08_01.xlsx). It is recommended that all columns be populated, with black compulsory and blue optional (explanations given in parenthesis):
+A separate Master List of Species / Taxa needs to be created for each group for which biodiversity data are served on FBIS. The Master List is ideally created before the consolidation of data so that the correct GBIF Taxonomic Backbone (https://www.gbif.org/dataset/d7dddbf4-2cf0-4f39-9b2a-bb099caae36c) is used for the data consolidation files. The taxonomy from GBIF should be used when the taxon is on GBIF. The FBIS team can check if the taxon is on GBIF using the following link: https://www.gbif.org/species/1 and insert the relevant species, genus, family etc. in the “Select a species” box.
+
It is important that the correct Taxon Rank should always be used to ensure correct uploading of the data files into FBIS.
+Note: It is recommended that significant time and resources are used to generate and refine the master list for each group (birds, fish, invertebrates etc) as much as possible before proceeding with data collation. This is the list around-which all of the occurrence data will pivot: the more accurate it is at the start, the more time you save in the long run when collating the biodiversity data for those taxa.
+Multiple sources of taxon occurrence data generally exist, although this is highly dependent on the country. Potential sources of biodiversity data include the following study reference categories:
+The following sections provide details of the recommended processes for sourcing taxon occurrence data from the different sources.
+Data from peer-reviewed scientific articles are best sourced by undertaking a literature search using Google Scholar. To ensure that relevant papers are identified, appropriate search term combination should be used. For example, for all native freshwater fishes in South Africa: “Genus species” & “South Africa” (where “Genus species” represents the scientific name for each taxon). Relevant articles are identified based on their titles, abstracts and methods section. The first 500 search results returned by Google Scholar should be assessed for relevancy. Each relevant article should be inspected for GPS coordinates – if these are not provided then the article may be catalogued but not included for data extraction (see 32.4 Extracting data and preparing bulk data for uploading into FBIS).
+Note: It is important that search terms are clearly-defined and consistent, so that the process is repeatable and defensible.
+University theses are easily searched using relevant university search engines. Often local experts also know of relevant theses and can be contacted directly. Where possible, electronic data should be sourced directly from individuals, as this saves significant time that would otherwise be occupied in transcription of paper to digital records during data consolidation.
+Technical and consultancy reports are often difficult to source and requires knowledge of local experts who have undertaken relevant studies. Where possible, electronic data should be sourced directly from individuals, as this saves significant time during data consolidation.
+Identify and contact relevant organisations who may have data to share that is already in a database. Data sharing agreements may be needed depending on the organisation.
+Identify individuals who may have data to share. Where possible, electronic data should be sourced directly from individuals, as this saves significant time during data consolidation.
+A Knowledge Database is a record of all study references from which data have been extracted for a particular group (e.g. birds, fish, wetland plants, invertebrates, algae, etc.). It is a useful record of all peer-reviewed scientific articles, theses and published reports for a group and each record should ideally be linked to a GitHub ticket to keep track of the data extraction (see 32.2.2 Using GitHub for managing data consolidation). An example of a Knowledge Database has been generated (FBIS Knowledge Database Example Template.xlsx). The following columns are included in the Knowledge Database, provided as excel file template that will be used for each FBIS group.
+Whilst abiotic data are not the main currency for FBIS, it is extremely useful to provide associated abiotic data when these have been collected concurrently with biotic data. For this reason, a number of abiotic spatial layers may be served, and a number of abiotic parameters may be included in the Data Upload Templates. These include aspects related to sampling method and effort, abundance, habitat/biotope, flow and physico-chemistry. Abiotic data associated with biodiversity data are included in the 32.4.2 Data Upload Templates. Examples are given below. These abiotic factors may need to be adapted depending on the taxonomic group being dealt with – for example bird abiotic data may need different habitat related attributes. These can easily be added in the administration section.
+Spatial data often take the form of shapefiles containing geometries representing physical properties or landscape features (e.g. catchments, habitat types etc.) and that have attribute data associated with them. These spatial layers may be hidden/shown for visualisation on the map by a user, while the data in these layers may be used to facilitate spatial filters which are used to select a subset of records based on the filter specified. Spatial layers and filters may be the same, although not always as it is dependent on the data attributes.
+Geocontext data are contextual data for any geographical point, sourced from relevant spatial layers and aggregated as properties of a site. Often spatial layers are used for generating geocontext data. The examples below are the spatial filters used in FBIS (see 32.2.1 Setting up a Dataset Tracker).
+Spatial layers, which may be turned on and off in the FBIS map, function as background layers upon which biodiversity data are displayed. The examples below are the spatial layers used in FBIS.
+Where databases and data platforms already exist, it is recommended that links (APIs) be created to access these data from the platform. Third party databases that FBIS links to includes data from Global Biodiversity Information Facility (GBIF) (taxonomy, diatom, invertebrate and fish data), the IUCN Red List of Threatened Species database, the MiniSASS database, which provides citizen science river health data, and DWS water quality database accessed via the Integrated Water Resources Decision Support System (InWaRDS 2020), and a ‘knowledge database’, which serves as a catalogue of metadata for all occurrence records. Data from certain modules of the Virtual Museum (Fitzpatrick Institute of African Ornithology, University of Cape Town 2021) are also included. GBIF and Virtual Museum data are harvested and served in FBIS, as a separate Data Source that complements collated data. In FBIS, freshwater species occurrence data available for South Africa in GBIF includes periodically-updated data from the South African Institute for Aquatic Biodiversity (SAIAB), as well as 'Research Grade' iNaturalist data (i.e. records from non-captive individuals, with a picture, locality and date, and with two or more IDs in agreement at species level). Invertebrate data includes both aquatic and aerial stages. The FBIS team need to provide guidance on the taxonomic groups for which GBIF data should be harvested, and should be based on the Master Lists (see Creating Taxonomic Master Lists).
+FBIS includes data capture forms for adding sites, fish, invertebrate and algae data, as well as associated abiotic data. However, these forms are intended for the capture of individual site visits, and at times, especially during the development phase of an information system, it is useful to be able to upload large amounts of data at a time. To ensure that bulk data are readily ingested into FBIS, a standardised Data Upload Template needs to be produced for each group. This will ensure that data are cleaned and provided in a standardised manner so that the data uploading process runs smoothly and so that the resultant FBIS platform serves quality data.
+Data extracted from peer-reviewed articles, theses and published reports need to be standardised to allow for comparison of data amongst studies. Each article/thesis/report needs to be inspected for GPS coordinates. Publications without GPS coordinates cannot be included in the information system. All relevant information, as specified in Table 1, 32.4.2 Data Upload Templates, pertaining to the occurrence record is then extracted from the publication and added to the Date Upload Template for the relevant group.
+Standardised data upload templates in excel have been generated for four biodiversity groups, namely anurans, fish, invertebrates and algae. Additional upload templates may be added as new biodiversity modules are added. These templates include a number of dropdown attributes. It is critical that all taxa in the Data Upload file for a particular biodiversity group are present in the Master List of Taxa for that group. If not, the upload process will not work. For this reason, it is recommended that where possible dropdown lists are used in the Data Upload files to ensure that all data entered in the sheet is valid. As an example, the Master List of fish species in South Africa has been included as dropdown list for the FBIS Fish Data Upload Template.
+ +The following data upload templates are provided:
+Many of the columns are the same for each group, although some additional columns are included for algae, and the dropdown options (e.g. biotopes) sometimes vary amongst groups. The common columns used in each group are given in Table 1. Relevant dropdown lists are provided in each template and additional group-specific columns are included in the relevant templates.
+Table 1. Column headers with details used in data upload templates
+| Column Header | +Details | +
|---|---|
| UUID | +A unique identifier for each record. Drag and copy the formula down. | +
| Original River or Wetland name Name | +Name given in study reference | +
| Original Site Code | +Site Code given in study reference | +
| FBIS Site Code | +Leave blank (autogenerated) | +
| Site description | +Description given in study reference | +
| Refined Geomorphological Zone | +As given in study reference (if available) - Select from dropdown options | +
| Latitude | +Decimal degrees with "-" in front & "," for decimal point | +
| Longitude | +Decimal degrees with "," for decimal point | +
| Sampling Date | +yyyy/mm/dd | +
| Kingdom | +Not necessary to fill in as they are derived from the Master Lists | +
| Phylum | +Not necessary to fill in as they are derived from the Master Lists | +
| Class | +Not necessary to fill in as they are derived from the Master Lists | +
| Order | +Not necessary to fill in as they are derived from the Master Lists | +
| Family | +Not necessary to fill in as they are derived from the Master Lists | +
| Genus | +Not necessary to fill in as they are derived from the Master Lists | +
| Species | +Not necessary to fill in as they are derived from the Master Lists | +
| Taxon | ++ |
| Taxon rank | +Select from dropdown options | +
| Present | +Fill in with "1" | +
| Sampling method | +Select from dropdown options | +
| Sampling effort measure | +Select from dropdown options | +
| Sampling effort value | ++ |
| Abundance measure | +Select from dropdown options | +
| Abundance value | +Leave blank if only presence data | +
| Record type | +Select from dropdown options | +
| Broad biotope | +Select from dropdown options | +
| Specific biotope | +Select from dropdown options | +
| Substratum | +Select from dropdown options | +
| Water Level | +Select from dropdown options | +
| Water Turbidity | +Select from dropdown options | +
| Embeddedness | +Select from dropdown options | +
| Depth | +Depth (m) | +
| Near Bed Velocity | +Near Bed Velocity (m/s) | +
| COND | +Conductivity (mS/cm) | +
| PH | +PH | +
| DOPER | +Dissolved Oxygen (%) | +
| DO | +Dissolved Oxygen (mg/L) | +
| TEMP | +Temperature (deg C) | +
| TURB | +Turbidity (NTU) | +
| Collector/Owner | +Full name | +
| Collector/Owner Institute | +Institute of collector/owner | +
| Author(s) | +Surname + Initials | +
| Year | +Year of study | +
| Source | +Source of data if from thesis or database | +
| Title | +Title of data source if thesis or published report | +
| Reference category | +Select from dropdown options | +
| URL | +Thesis handle, or article link if no DOI available | +
| DOI | +DOI for reference ( e.g. 10.2989/16085914.2018.1491385) | +
| Document Upload Link | +Link to "Documents" page on FBIS after uploading PDF of published report | +
| Notes | +Any details related to sampling, species, life form etc. | +
All biodiversity data served on FBIS need to have associated Metadata (Figure 2). A Source Reference Management system have been incorporated in FBIS. This metadata allows the users to establish exactly where the data originated from and to navigate to the study reference if desired. As per Sources of biodiversity data, five types of study references are served, namely peer-reviewed scientific articles, theses, published reports, databases and unpublished data. This is described in a separate document: Managing Source References.
+Figure 2. Metadata Table
+
Dallas HF, Shelton JM, Sutton T, Tri Ciputra D, Kajee M and Job N. 2022. The Freshwater Biodiversity Information System (FBIS) – mobilising data for evaluating long-term change in South African rivers, African Journal of Aquatic Science 47(3): 291-306, DOI: 10.2989/16085914.2021.1982672
+ +Freshwater Biodiversity Information System (FBIS). 2022. Downloaded from https://freshwaterbiodiversity.org on [current date]
+ +Freshwater Biodiversity Information System (FBIS). 2022. FBIS User Manual. Prepared by the Freshwater Research Centre and Kartoza.
All existing taxon occurrence data are harvested per Taxon Group from the Global Biodiversity Information Facility (GBIF). This section outlines the steps for harvesting GBIF data.
+Only registered users with super user status are able to do this, typically the administrators .
+The Master List of Taxa for a Taxon Group is used to facilitate harvesting of data from GBIF, thereby ensuring that the correct taxa are included on the information system.
+Click on your profile and select Harvest from GBIF.
+
Select the Taxon Group using the dropdown and click Start harvesting.
+
You can keep track of progress. The more taxa in the master list, the longer the time needed for harvesting data from GBIF. You can keep it running in the background and continue with other work as it harvests the data.
+
You can view the GBIF data harvested via the Download Logs.
+
This section provides a guide for biodiversity data administrators to mobilize and ingest biodiversity data. The steps outlined are sequential and each provides details on the process and key considerations.
+++Only registered users with super user status, typically the site administrators, are able to view the administration sections and undertake the following steps related to the mobilization and ingestion of biodiversity data.
+
The sections covered include:
+Several backend tables can be updated and managed by administrators, including the Biodiversity Information Management System (BIMS), and are accessible via the Admin Page. Provided here, is a list of actions related to the Site Administration including the BIMS table management that an administrator (super user status) may need to edit or check. Currently, only the tables that the administrator needs to be able to revise have been described, and not all the tables in the Site Administration and BIMS. They are described chronologically as they appear in Site Administration. This document will continually need to be updated as new administration functions are added.
+Link to specific sub-sections in BIMS as well as other admin tasks:
+Managing BIMS Admin tables
+Here you manage the broad biotope categories, description and order; the specific biotope categories, description and order; and the substratum. These biotopes are initially populated by the biodiversity data upload files, where each biotope is specified in the dropdowns. Details are provided below. Certain biotopes and substrata may be associated with one or more modules. As more biodiversity modules are added, it may be necessary for the administrator to update biotopes.
+| Module | +Broad Biotope | +Specific Biotope | +Substratum | +
|---|---|---|---|
| All | +Unspecified | ++ | + |
| All | +Mixed | ++ | + |
| Algae, invertebrates, anurans | +Stones In Current | ++ | + |
| algae, invertebrates, anurans | +Stones Out Of Current | ++ | + |
| algae, invertebrates, anurans | +Marginal Vegetation | ++ | + |
| algae, invertebrates, anurans | +Aquatic Vegetation | ++ | + |
| algae, invertebrates, anurans | +Gravel/Sand/Mud | ++ | + |
| algae, invertebrates | +Artificial substrate | ++ | + |
| Fish only | +Slow-Shallow | ++ | + |
| Fish only | +Slow-Deep | ++ | + |
| Fish only | +Fast-Shallow | ++ | + |
| Fish only | +Fast-Deep | ++ | + |
| All | ++ | Backwater | ++ |
| All | ++ | Bedrock | ++ |
| All | ++ | Cascade | ++ |
| All | ++ | Chute | ++ |
| All | ++ | Detritus | ++ |
| All | ++ | Mixed | ++ |
| All | ++ | Pool | ++ |
| All | ++ | Rapid | ++ |
| All | ++ | Riffle | ++ |
| All | ++ | Run | ++ |
| All | ++ | Slackwater | ++ |
| All | ++ | Unspecified | ++ |
| All | ++ | Waterfall | ++ |
| All | ++ | + | Unspecified | +
| All | ++ | + | Mixed | +
| All | ++ | + | Bedrock | +
| All | ++ | + | Boulder | +
| All | ++ | + | Cobble | +
| All | ++ | + | Detritus | +
| All | ++ | + | Gravel | +
| All | ++ | + | Pebble | +
| All | ++ | + | Sand | +
| All | ++ | + | Silt/Mud/Clay | +
If these have not been included in the data occurrence upload files, then they are blank. New biotopes can be added by clicking the “+ Add biotope”.
+Here you manage the physico-chemical data including the Chem Code (NB this needs to match the column in the physico-chemical data upload template), chem description, chem unit, whether the variable needs to be shown in abiotic form (abiotic list), minimum and maximum values. New chemistry units can be added by clicking the “+ Add chemistry unit”.
+
Changes can be made to each variable by clicking on the relevant Chem code and editing the appropriate field. Here one can also specify the number of decimal places.
+
Here you manage the download request purposes that a user chooses when requesting a download of a graph or csv file. New purposes can be added by selecting “Add download request purpose” and the sort order can be updated.
+
Here you can see all download requests from users, including details of the requester, resource type (csv, table, chart), resource name and purpose (as specified in the download request purposes). One can find out further details of the request by clicking on the Request date link, which opens up a second form. This is useful to track the progress of the large request downloads.
+
Here you manage the endemism categories including the Name (what is shown on the dashboard), description and display order. The endemism categories are added during the uploading of the taxonomic master lists. Note that if the description is used in the master list, then this will be shown on the side panel and / or dashboard. It is important to always upload the Name only.
+
Each endemism category can be edited by clicking on the Name
+
Here you can view all the uuids - this is a unique id for each occurrence record. It also allows the administrator to delete a specific record based on it uuid.
+
Here you can manage the Conservation status categories for global and national. Global is pulled down from the IUCN, while national is from SANBI. Status’s only applicable to national need to be opened and national checked. To change a status click on category.
+
Here you can manage the spatial layers shown in the side panel and dashboards, as well as the display and filter orders. This is done by clicking on the ID link, which opens up a separate form for each spatial layer.
+
Here you can change the display order of the spatial filters.
+
Here you can manage the spatial layers and groups, which relate to geocontext. Each layer can be opened to view detail.
+
Here you manage what is seen on the Side panel and Dashboard for a single site. Information included in the dashboards is indicated with a green tick.
+
To change what is displayed click the ID Number and check or uncheck the box for each. Note that there are some extra aspects that still need clarifying related to order etc.
+
Here you can view sites, filter for specific site and update site codes.
+
Here we are also able to update the geocontext data for each site or selection of sites.
+
Here you manage the order that spatial layers are shown. This includes viewing and/or editing the order, name, wms url and Wms layer name. By clicking on the order, the details of the layer can be viewed and edited. Only administrators experienced in geocontext and GGIS should edit this as it links directly to these components.
+
***To Be Updated***
Here you manage the sampling methods used for collection of biodiversity occurrence data. These sampling methods are initially populated by the biodiversity data upload files, where each sampling method is specified in the dropdowns. Details are provided below.
+For each sampling method the administrator needs to select the taxon group or groups that the method is associated with and certain sampling methods may be associated with one or more taxon groups / modules. As more biodiversity modules are added, it may be necessary for the administrator to update the sampling methods.
+| Module | +Sampling method | +
|---|---|
| Invertebrates only | +Baited Line | +
| Invertebrates only | +Box/Surber | +
| Invertebrates only | +Drift Net | +
| Invertebrates only | +Kick Net | +
| Invertebrates only | +Light Trap | +
| Invertebrates only | +Stone | +
| Invertebrates, fish | +Hand Net | +
| Fish only | +Fyke net | +
| Fish only | +Gill net | +
| Fish only | +Rod and line angling | +
| Fish only | +Seine net | +
| Fish only | +Snorkelling | +
| Fish, anurans | +Underwater video analysis | +
| Fish, anurans | +Electro-fishing | +
| Fish, anurans | +Visual survey | +
| Anurans | +Active acoustic survey | +
| Anurans | +Passive acoustic survey | +
| Anurans | +Baited trapping | +
| Anurans | +Non-baited survey | +
| All | +Unspecified | +
| All | +Multiple | +
Changes can be made to each sampling method by clicking on the Sampling method and editing the name, order and Taxon group it is appropriate to. To select more than one taxon group click Control Select simultaneously. If these have not been included in the data occurrence upload files, then they are blank. New sampling methods can be added by clicking the “+ Add sampling method”.
+We have also added functionality to merge sampling methods, in the event that the same sampling method is added, but with a slight variation. For example:
+
To merge these two or more sampling methods, first you need to verify the correct one, by opening the method and ticking the verify box.
+
Then you use the select “Merge sampling methods” and click go.
+
Here you manage several components related to the setting of the site (i.e. webpage, url for the information systems, e.g. FBIS, RBIS, ORBIS etc.). Details of the sections that an administrator can change are provided below.
+Site notice can be changed in the Site settings section.
+
You can specify the readme file that is bundled with the downloaded occurrence data.
You can specify the taxonomic upload template for the Master lists. This is then downloadable on the Upload – Taxonomic data.
+
You can specify the occurrence upload template for the occurrence data. This is then downloadable on the Upload – Occurrence data.
+
You can view and/or edit the disclaimer form text and disclaimer doc text.
+
You can enable or disable the third party layer as not all information systems have links to third party data
+
You can enable or disable sass as not all information systems have sass data
+
You can enable or disable water temperature data as not all information systems have water temperature data
+
You can enable or disable download request approval. If this is disabled then the user can download the data without waiting for approval from the administrator.
+
You can enable or disable the module summary on the landing page dashboard. This is not applicable to FBIS, only RBIS and ORBIS.
+
You can enable or disable the remove all occurrence tool in Taxon Management. This should never be activated on the live/production site as clicking the Remove all button, will delete all the occurrence data for the module. It can be enabled on the testing site as this allows administrators to practice the creation of new modules, uploading of taxonomic master lists and the uploading f occurrence data.
+
You can view and/or edit the copyright text that is visible at the bottom of the landing page.
+
Generally it is easiest to manage source references (i.e. the metadata associated with each occurrence record).
+
However, on occasions, issues arise whereby the source reference is duplicated, possibly because of a small typo during data capture. In the Admin - Source references – section it is possible to merge two source references. One does this by finding the two relevant source reference, opening the correct one and selecting “Verify”, the checking the box next to the two (or more) references to be merged, and using the Merge from the dropdown lists, the Go. Note that the Source reference needs to be the same type to be able to merge.
+
Here you manage all aspects related taxa within the information system. Most of this is done easily within Taxon Management, but there are some actions that can only be done within this table, including deleting a taxon (this cannot be done if occurrence data are associated with it), merging taxa and updating taxa (when one taxon is a synonym of another).
+The table includes the Canonical Name (also referred to as the "true name”), the Link to gbif, the Scientific Name, the Taxonomic Rank, the Parent, the Import date, the Taxonomic Status, the Legacy Canonical Name, and whether the taxon has been Verified. Ultimately all taxa in the information system should be verified.
+
Clicking on the canonical name opens up the Change Taxonomy form for the selected species. Note that this is same as that accessed within Taxon Management.
+
A search field and filters are also included to assist you to navigate.
+
To delete a taxon, click the check box, and select Delete selected taxon, and click GO
+
There is a check, and if you click, Yes, I am sure, then the taxon will be deleted
+
Sometimes errors are picked up in the taxa, for example there are two taxa that are the same. One the needs to merge these taxa. Prior to merging, the correct taxon needs to be checked and the verified button checked. Then to merge the two taxa, click the check box, and select Merge taxa, and click GO.
Updating is used when one wants to update a synonym with the accepted name. Prior to updating, the accepted taxon needs to be checked and the verified button checked. Then to update the synonym, click the check box of both taxa, and select Update taxa, and click GO. This functionality is currently being refined.
+Here you manage the taxon groups added to the information systems. To note is the need to add the singular name so that it is correct in the Add XXXX data form.
+
This is access outside of the BIMS section, in Flat Pages. From here you can update the “About us”, Citation guidelines and Help page.
+
Text for the About Us on the menu bar can be modified here: +https://freshwaterbiodiversity.org/admin/flatpages/flatpage/3/change/
+
Text for the Citation on the landing page can be modified here: +https://freshwaterbiodiversity.org/admin/flatpages/flatpage/3/change/
+Text for the Help on the menu bar can be modified here: +https://freshwaterbiodiversity.org/admin/flatpages/flatpage/2/change/
+Here's how to update the link to the FBIS manual:
+
Ok, and then click SaveGet the url for the FBIS Manual by opening Source References and right clicking the green title, and choose 'Copy link address'. Then insert this url into the URL in the Link tab and save.
+
Details of all users are visible here and can be edited as needed. When a user first registers they are activated by clicking the Permission – Active box.
+Several filters have been included to manage and find users
+
A specific administration module has been developed to allow administrators to manage metadata and citations associated with each biological occurrence record.
+
Only registered users with super user status are able to access Source References, typically the administrators.
+All biodiversity data served need to have associated Metadata, which is visible in the metadata table in the dashboards. This metadata allows the users to establish exactly where the data originated from and to navigate to the study reference if desired.
+
Multiple sources of taxon occurrence data generally exist, although this is highly dependent on the country. Potential sources of biodiversity data include the following source reference categories:
+The following sections provide details of the recommended processes for sourcing taxon occurrence data from the different reference categories. This is done by all users adding data and by administrators.
+Data from peer-reviewed scientific articles are best sourced by undertaking a literature search using Google Scholar. To ensure that relevant papers are identified, appropriate search term combination should be used. For example, for all native freshwater fishes in South Africa: “Genus species” & “South Africa” (where “Genus species” represents the scientific name for each taxon). It is important that search terms are clearly-defined and consistent, so that the process is repeatable and defensible.
+University theses are easily searched using relevant university search engines. Often local experts also know of relevant theses and can be contacted directly. Where possible, electronic data should be sourced directly from individuals, as this saves significant time that would otherwise be occupied in transcription of paper to digital records during data consolidation.
+Technical and consultancy reports are often difficult to source and requires knowledge of local experts who have undertaken relevant studies. Where possible, electronic data should be sourced directly from individuals, as this saves significant time during data consolidation.
+Identify and contact relevant organisations who may have data to share that is already in a database. Data sharing agreements may be needed depending on the organisation. For organisation that regularly add data it is useful to set up a database in the organisation’s name.
+Identify individuals who may have data to share. Where possible, electronic data should be sourced directly from individuals, as this saves significant time during data consolidation.
+Source reference system can store either an electronic document (e.g. by attaching a PDF to the document record) or a link to an online resource (URL). The order of preference should be:
+Source references are either added when data are added using the data capture forms on FBIS, or when uploading occurrence data using the data upload excel file. (See Preparing and checking an Occurrence Data File before uploading).
+When adding data, three data capture forms are shown in sequence, namely 1) an occurrence record form, where you capture which taxa were present; 2) an abiotic data form where you capture physico-chemical and other abiotic data; and 3) a source reference for records form, where you capture the source reference or metadata for the biological record.
+
Select the reference category and insert the DOI or URL and click the search button. The citation is then retrieved via an online citation management system and inserted. Click Submit to save.
+
Select the reference category and select from the dropdown list of titles, if the published report or thesis is already uploaded, or select “Upload new” to add a new published report or thesis.
+
When uploading a new published report or thesis, complete the fields using the format indicated including Author(s), Year, Source, Title, Description (if desired) and Url or upload file. Confirm that you are owner of the document being added and Upload. This is then submitted.
+
Select the reference category and select from the dropdown list of databases, if the database is already created, or select “Add new” to add a new database.
+
When adding a new database, complete the name and provide a description. Add the url if it exists and click create. Add notes if desired.
+
Select the reference category and select from the dropdown list under notes. If the unpublished dataset exists, select the unpublished dataset name, or if the unpublished dataset needs to be created, select “Add new” to add a new unpublished dataset. In the notes, add the name of the person, details of the study and date if possible or applicable.
+
Where data are uploaded using the Data Upload Templates, the data capturer needs to specify the following:
+When adding occurrence data using the upload excel files, the following columns are populated for each reference category:
+Errors can arise when source references are added to the information system by users. These can be picked up and fixed by undertaking various filters, checking and edits, including those listed below.
+
Once the source reference has been found, it can be updated, deleted (only if there are not records associated with it), and the Document ID can be copied. This is needed when uploading occurrence records using the excel template.
+
By clicking on the records button you can check exactly which sites and data are linked to the source reference.
A taxonomic Master List is a list of all species and/or taxa within a particular group such as birds, fish, invertebrates, wetland plants, algae, etc. This section highlights issues and specific checks to improve accuracy of the Master List. The format of the Master List is important to ensure consistency for ingestion of data into the information system. The columns included in the Master Lists are detailed in the Data Management Guidelines.
+++Only registered users with super user status are able to do this, typically the administrators.
+
A taxonomic Master List is a list of all species and/or taxa within a particular group such as birds, fish, invertebrates, wetland plants, algae, etc. For some groups a species list is easy to produce as species level is commonly identified in studies (e.g. birds, fish). For other groups, the taxonomic level (family, genus, species etc) varies considerably from study to study, and thus it is recommended that the lowest taxonomic level is used and that Taxon is used in preference to Species (e.g. invertebrates, algae).
+The purpose of the Master List is threefold:
+The generation of a Master List requires consultation with available resources, relevant publications and experts. A Master List is intended to be an updatable resource, improved and added to as new data and studies are published, or new taxa are described. If no species lists are available for a country then the GBIF Taxonomic Master List may be generated by extracting data from GBIF. This Master List should then ideally be checked and validated for accuracy by the FBIS team.
+The format of the Master List is important to ensure consistency for ingestion of data into the information system. The following columns are included in the Master Lists, provided as excel file template that will be used for each FBIS group (FBIS Master List of Taxa Template.xlsx). It is recommended that all columns be populated, with black compulsory and blue optional (explanations given in parenthesis):
+
+* Common name
+* Former scientific names
A separate Master List of Species/Taxa needs to be created for each group for which biodiversity data are served on FBIS. The Master List is ideally created before the consolidation of data so that the correct GBIF Taxonomic Backbone (https://www.gbif.org/dataset/d7dddbf4-2cf0-4f39-9b2a-bb099caae36c) is used for the data consolidation files. The taxonomy from GBIF should be used when the taxon is on GBIF. The FBIS team can check if the taxon is on GBIF using the following link: https://www.gbif.org/species/1 and insert the relevant species, genus, family etc. in the “Select a species” box.
+
Taxa that are not on GBIF may be included in a Master List but the Source (Details of the publication source for this taxon) needs to be provided. Unfortunately several taxa may be missing from GBIF which, while it is the best available, is not always 100% correct.
+There is also another platform that is useful, the Freshwater Animal Diversity Assessment (FADA) Project (http://fada.biodiversity.be/). FADA is the taxonomic backbone for its Freshwater Biodiversity Data Portal. One is able to consult and download FADA data, although it is not always up to date.
+Important notes and common errors:
+It is important that the correct Taxon Rank is always used to ensure correct uploading of the data files. Taxon Rank is case sensitive so Species will upload but species will fail. Always ensure the correct Taxon Rank is applied by using the dropdown list. There should be no spaces in SubClass, SubOrder, SubFamily, SubSpecies.
+The column On GBIF: If the taxon is on GBIF, this must be Yes, then it is not necessary to add the GBIF URL. However, it is recommended that the GBIF URL be added to ensure the correct taxon is added. However, if the taxon is not on GBIF, then this must be No. Always include the full taxonomic hierarchy for all taxa (Kingdom, Phylum, Class, Order, etc.).
+Note: It is recommended that significant time and resources are used to generate and refine the master list for each group (birds, fish, invertebrates etc) as much as possible before proceeding with data collation. This is the list around-which all of the occurrence data will pivot: the more accurate it is at the start, the more time you save in the long run when collating the biodiversity data for those taxa.
+To ensure the Master list is accurate, several steps should be taken before uploading taxonomic data. After consolidating the master list, you should check the following:
+Apply filters for checking the data by highlighting the header row, clicking Data, Filter. All columns should be checked for consistencies and typos. Systematically work from column A to W. In particular, check consistency of the Taxon Rank and taxonomic hierarchy (Kingdom, Phylum, Class, Order, Family, Genus, Species, SubSpecies, Taxon).
+
It is important to check the GBIF taxonomy for accepted names and synonyms. For example, in the avian master list, Ardea alba - is the accepted name, whereas Casmerodius albus is the synonym. Preferably only accepted names should be included in the Master List of Taxa.
+
Taxa should be checked for duplicates by highlighting the Taxon column, and from the Home Menu, selecting Conditional Formatting, Highlight Cells Rules, Duplicate Values.
+
GBIF URLs should also be checked for duplicates by highlighting the GBIF URL column, and from the Home Menu, selecting Conditional Formatting, Highlight Cells Rules, Duplicate Values.
+Note: All taxa can be updated after ingestion through the Taxon Management section.
+Delete blank rows and columns. Lastly, ensure that there are no extra blank rows or columns, by deleting them.
+
It may be desirable to add attributes for specific taxon groups such as “Water dependence” (Highly dependent, Moderately dependent, Minimally dependent, Terrestrial). These additional attributes are assigned to each taxon during the uploading of the master lists as long as the additional attribute is added in Taxon Management before uploading.
+This is done in the Edit Module form, Add attribute. The attribute needs to match the attribute column header in your Master List for uploading.
+
FBIS includes data capture forms for adding sites, fish, invertebrate and algae data, as well as associated abiotic data. However, these forms are intended for the capture of individual site visits, and at times, especially during the development phase of an information system, it is useful to be able to upload large amounts of data at a time. To ensure that bulk data are readily uploaded into FBIS, a standardised Data Upload Template needs to be produced for each group. This will ensure that data are cleaned and provided in a standardised manner so that the data uploading process runs smoothly and so that the resultant FBIS platform serves quality data.
+Standardised data upload templates in excel have been generated for four biodiversity groups, namely anurans, fish, invertebrates and algae. Additional upload templates may be added as new biodiversity modules are added. These templates include a number of dropdown attributes. It is critical that all taxa in the Data Upload file for a particular biodiversity group are present in the Master List of Taxa for that group. If not, the upload process will not work. For this reason, it is recommended that where possible dropdown lists are used in the Data Upload files to ensure that all data entered in the sheet are valid. As an example, the Master List of fish species in South Africa has been included as dropdown list for the FBIS Fish Data Upload Template.
+The following data upload templates are provided:
+Many of the columns are the same for each group, although some additional columns are included for algae, and the dropdown options (e.g. biotopes) sometimes vary amongst groups. The common columns used in each group are given in Table 1. Relevant dropdown lists are provided in each template and additional group-specific columns are included in the relevant templates. Those column headers in red have to be filled in the occurrence upload file. See section on Check the Source Reference for details of which columns are relevant for different reference categories. Those column headers shaded green use dropdown lists in the excel file. These can be modified in the Admin page (BIMS).
+Table 1. Column headers with details used in data upload templates
+| Column Header | +Details | +
|---|---|
| UUID | +A unique identifier for each record. Drag and copy the formula down. | +
| Original River or Wetland Name | +Name given in study reference | +
| Original Site Code | +Site Code given in study reference | +
| Site Code | +Leave blank (autogenerated) | +
| Site description | +Description given in study reference | +
| Refined Geomorphological Zone | +As given in study reference (if available) - Select from dropdown options | +
| Latitude | +Decimal degrees with "-" in front & "," for decimal point | +
| Longitude | +Decimal degrees with "," for decimal point | +
| Sampling Date | +yyyy/mm/dd | +
| Kingdom | +Not necessary to fill in as they are derived from the Master Lists | +
| Phylum | +Not necessary to fill in as they are derived from the Master Lists | +
| Class | +Not necessary to fill in as they are derived from the Master Lists | +
| Order | +Not necessary to fill in as they are derived from the Master Lists | +
| Family | +Not necessary to fill in as they are derived from the Master Lists | +
| Genus | +Not necessary to fill in as they are derived from the Master Lists | +
| Species | +Not necessary to fill in as they are derived from the Master Lists | +
| Taxon | ++ |
| Taxon rank | +Select from dropdown options | +
| Present | +Fill in with "1" | +
| Sampling method | +Select from dropdown options | +
| Sampling effort measure | +Select from dropdown options | +
| Sampling effort value | ++ |
| Abundance measure | +Select from dropdown options | +
| Abundance value | +Leave blank if only presence data | +
| Record type | +Select from dropdown options | +
| Broad biotope | +Select from dropdown options | +
| Specific biotope | +Select from dropdown options | +
| Substratum | +Select from dropdown options | +
| Water Level | +Select from dropdown options | +
| Water Turbidity | +Select from dropdown options | +
| Embeddedness | +Select from dropdown options | +
| Depth | +Depth (m) | +
| Near Bed Velocity | +Near Bed Velocity (m/s) | +
| COND | +Conductivity (mS/cm) | +
| PH | +PH | +
| DOPER | +Dissolved Oxygen (%) | +
| DO | +Dissolved Oxygen (mg/L) | +
| TEMP | +Temperature (deg C) | +
| TURB | +Turbidity (NTU) | +
| Collector/Owner | +Full name | +
| Collector/Owner Institute | +Institute of collector/owner | +
| Author(s) | +Surname + Initials | +
| Year | +Year of study | +
| Source | +Source of data if from thesis or database | +
| Title | +Title of data source if thesis or published report | +
| Reference category | +Select from dropdown options | +
| URL | +Thesis handle, or article link if no DOI available | +
| DOI | +DOI for reference ( e.g. 10.2989/16085914.2018.1491385) | +
| Document Upload Link | +Link to "Documents" page on FIBbio after uploading PDF of published report | +
| Notes | +Any details related to sampling, species, life form etc. | +
It is recommended that separate data upload files be created for each Source Reference, with each linked to a GitHub ticket. This ensures accurate management of data preparation and management.
+To ensure that data are accurate, several steps should be taken before uploading occurrence data. After consolidating the occurrence data in the data file, you should check the following:
+Apply filters for checking the data by highlighting the header row, clicking Data, Filter
+
UUID: This is a unique id for each occurrence record. It needs to be copied and pasted so that the formula used to generate it is saved as a number.
+The UUID formula is available here: +
=LOWER(CONCATENATE(DEC2HEX(RANDBETWEEN(0,POWER(16,8)),8),"-",DEC2HEX(RANDBETWEEN(0,POWER(16,4)),4),"-","4",
+DEC2HEX(RANDBETWEEN(0,POWER(16,3)),3),"-",DEC2HEX(RANDBETWEEN(8,11)),DEC2HEX(RANDBETWEEN(0,POWER(16,3)),3),
+"-",DEC2HEX(RANDBETWEEN(0,POWER(16,8)),8),DEC2HEX(RANDBETWEEN(0,POWER(16,4)),4)))
+Systematically check each column using the dropdown arrows, and look for inconsistencies. Some common issues include, #num in UUID column instead of the UUID, incorrect spelling in the Site description column (e.g. Gakiriro wetland, Gakirirowetland), latitude with missing “-“ (e.g. 2.60059 as latitude is incorrect – should be -2.60059), longitude.
+Also check that all sites fall within the country boundary so that Site Codes may be generated correctly and geocontext data harvested for each site.
+
+
Check that the sampling date is in the correct format: yyyy/mm/dd. If the format is not correct then the upload will not work.
+Check that all taxa are correct and are present in the Master List. If the dropdown of master taxa list was used then this should not be an issue. Check that the Taxon rank is correct. It is important that the correct Taxon Rank is always used to ensure correct uploading of the data files. Taxon Rank is case sensitive so Species will upload but species will fail. Always ensure the correct Taxon Rank is applied by using the dropdown list. There should be no spaces in SubClass, SubOrder, SubFamily, SubSpecies.
+
Check presence is all “1”, check sampling method is correct.
+
+
Check Collector/Owner and Collector/Owner Institute. Ideally CAPITALS should not be used, First name Surname if known. Do not use middle initial and punctuation.
+
Check the Source Reference (Author(s), Year, Source, Title, Reference category, URL, DOI, Document Upload Link). For each study reference type, you need to populate the following columns:
+Check format of Author(s). It needs to be: Surname + Initials, no punctuation. (e.g. Tumushimire L, Mindje M, Sinsch U & Dehling JM not Lambert Tumushimire, Mapendo MINDJE, Prof. Ulrich Sinsch & Julian Maxmillian Dehling). It is important to get the authors correct (e.g. Sinsch Ulrich and Dehling, J. Maximilian, Lümkemann Katrin, Rosar Katharina, Christiane Schwarz should be Sinsch U, Lümkemann K, Rosar K, Schwarz C & Dehling M as per the doi).
+
Check the Date: This is the publication date (so 2012-2013 should be 2019 as this is when the article was published - Ecology and Evolution. 2019. Same with all other data from this study).
+
Check the Source. Please note when to include source or not, and what to include. (e.g. Mindje, M., Tumushimire, L., & Sinsch, U. (2020). Diversity assessment of anurans in the Mugesera wetland (eastern Rwanda): impact of habitat disturbance and partial recovery. Salamandra, 56, 27-38. Should be Salamandra)
+
Check the Title. For Peer-reviewed scientific article the Title is the title of the article, for Published reports or theses, it is the title of the thesis. Unpublished data don’t need a title.
+
Check all Reference Categories are correct: options include:
+
Check URL and DOI. Use a DOI if it is available, URL – only needed for Peer-reviewed scientific article if there is no DOI. For the DOI you only need to include the number part, so 10.1080/15627020.2012.11407524, not https://doi.org/10.1080/15627020.2012.11407524.
+
+
Check the document upload link is correct. Note the Document Upload Link is obtained after the report is added. Reports are only uploaded when there is no DOI or URL to link the data to.
+Checking for duplicate occurrence records. Use this formula for checking for duplicates. This is a combination of Site description, latitude, longitude, sampling date, Taxon, sampling method, author, year, source and title. Copy and paste the formula below into a new column at the end and name it “Duplicate check”.
+ +Then copy and paste the formula down to the end of the data rows. Then Highlight the column, and from the Home menu, select Conditional Formatting, Highlight Cells Rules, Duplicate Values.
+
Any duplicates will be highlighted. Check and delete duplicate occurrence records. Then delete the Duplicate Check column.
+Delete blank rows and columns. Lastly, ensure that there are no extra blank rows or columns, by deleting them.
+
Remove the data filter, save the file in excel, and save the file as csv file.
+
Click on your profile and select Upload Occurrence Data
+
Select the Taxon Group using the dropdown and browse to the file containing the occurrence data for the taxon group, click upload
+
++Note: The Excel file needs to be saved as a csv using the following option:
+
Progress is shown:
+
A Success file will indicate occurrence records uploaded to the system. An Error file will give details of occurrence records not uploaded. The last column in this csv file provides an indication of the reason the occurrence record was not uploaded. The administrator then needs to check the data and correct before uploading again.
+Common errors:
+Occurrence records may be updated by uploaded corrected records in the csv file. As long as the UUID is the same then the old occurrence record will be updated.
+New occurrence records may be added by repeating the steps from (4), to upload the additional occurrence records for the Taxon Group.
+Note that once the occurrence data has been uploaded, geocontext data (i.e. information about the site such as province, catchment etc.) are automatically populated for each site. This takes time and it is recommended that the next step (i.e. harvesting from GBIF), is done at least 24 hours after uploading occurrence data.
This section explains how an administrator or user adds physico-chemical data to a site or prepares an excel template for bulk uploading of physico-chemical data for multiple sites and or sampling dates. In either case it is important to note that physico-chemical data can only be added for a specific variable, if that variable already exists in the Admin/Bims/Chemistry units table. If the variable is missing from this table, it will not show in the list and the upload will fail. This is described in detail in a separate document: 11. Managing BIMS Admin tables
+A data capture form has been added for uploading physico-chemical data to a single site. The user needs to follow the following steps:
+Adding physico-chemical data.
+
A physico-chemical template has been created for uploading physico-chemical records for multiple sites and sampling dates. Each line represents a unique Site-Sampling date. The template provided includes the full list of variables currently in the FBIS system, however these can be modified for the needs of the RBIS.
+Here is the full list of columns included in the physico-chemical template. It resembles the occurrence data upload template for the more generic column headers.
+| UUID | +
|---|
| Original Wetland Name | +
| Original Site Code | +
| Site Code | +
| Site description | +
| Latitude | +
| Longitude | +
| Sampling Date | +
| Collector/Owner | +
| Collector/Owner Institute | +
| Author(s) | +
| Year | +
| Source | +
| Title | +
| Reference category | +
| URL | +
| DOI | +
| Document Upload Link | +
| Notes | +
Proceeding this is each variable (with the header as the Chem code), each in a separate column. Here is the master list of physico-chemical variables currently in FBIS, giving the Chem code, description and unit of measurement.
+| Chem code | +Chem description | +Unit | +
|---|---|---|
| AL | +Aluminium | +mg/l | +
| AS | +Arsenic | +mg/l | +
| B | +Boron | +mg/l | +
| BA | +Barium | +mg/l | +
| BE | +Beryllium | +mg/l | +
| BOD | +Biological Oxygen Demand | +mg/l (5 days) | +
| CA | +Calcium | +mg/l | +
| CACO3 | +Total hardness | +mg/l | +
| CD | +Cadmium | +mg/l | +
| CL | +Chloride | +mg/l | +
| CO | +Cobolt | +mg/l | +
| CO3 | +Carbonate | +mg/l | +
| COD | +Chemical Oxygen Demand | +mg/l | +
| COL | +Colour | +APHA units | +
| COND | +Conductivity | +mS/m | +
| CR | +Chromium | +mg/l | +
| CU | +Copper | +mg/l | +
| DIN | +Nitrogen: dissolved inorganic (NH4+NO3+NO2)-N | +mg/l | +
| DO | +Oxygen: dissolved | +mg/l | +
| DOC | +Carbon: dissolved organic | +mg/l | +
| DON | +Nitrogen: dissolved organic | +mg/l | +
| DOPER | +Oxygen: dissolved: percentage saturation | +% | +
| ECOLI | +Coliforms: Escherichia coli (E. coli) | +Cfu/100ml | +
| F | +Fluoride | +mg/l | +
| FAECAL C | +Coliforms: Total faecal colifoms | +Cfu/100ml | +
| FE | +Iron | +mg/l | +
| HCO3 | +Bicarbonate | +mg/l | +
| HG | +Mercury | +mg/l | +
| K | +Potassium | +mg/l | +
| KJN | +Nitrogen: kjeldahl | +mg/l | +
| MG | +Magnesium | +mg/l | +
| MN | +Manganese | +mg/l | +
| MO | +Molybdenum | +mg/l | +
| NA | +Sodium | +mg/l | +
| NH3-N | +Nitrogen: ammonia | +mg/l | +
| NH4-N | +Nitrogen: ammonium | +mg/l | +
| NI | +Nickel | +mg/l | +
| NO2-N | +Nitrogen: nitrite | +mg/l | +
| NO2+NO3-N | +Nitrogen: Nitrate + nitrite | +mg/l | +
| NO3-N | +Nitrogen: nitrate | +mg/l | +
| PB | +Lead | +mg/l | +
| pH | +pH | ++ |
| PHALK | +Alkalinity: phenolthalein | +meq/l | +
| PHEN | +Phenols | +mg/l | +
| PO4-P | +Phosphorus: orthophosphate | +mg/l | +
| POM | +Particulate organic matter | +mg/l | +
| SALINITY | +Salinity | +% | +
| SD | +Secchi depth | +m | +
| SIO2 | +Silica | +mg/l | +
| SIO4 | +Orthosilicate | +mg/l | +
| SO4 | +Sulphate | +mg/l | +
| SR | +Strontium | +mg/l | +
| SRP | +Phosphorus: soluble reactive | +mg/l | +
| TAL | +Alkalinity: total | +meq/l | +
| TDS | +Total dissolved solids | +mg/l | +
| TEMP | +Temperature | +deg C | +
| TI | +Titanium | +mg/l | +
| TIC | +Carbon: total inorganic | +mg/l | +
| TIN | +Nitrogen: total inorganic | +mg/l | +
| TOC | +Carbon: total organic | +mg/l | +
| TORGS | +Total suspended solids: organics | +mg/l | +
| TORGS% | +Total suspended solids: organic fraction (%) | +% | +
| TOT-N | +Nitrogen: total | +mg/l | +
| TOT-P | +Phosphorus: total | +mg/l | +
| TSS | +Total suspended solids | +mg/l | +
| TURB | +Turbidity | +NTU | +
| V | +Vanadium | +mg/l | +
| ZN | +Zinc | +mg/l | +
| ZR | +Zirconium | +mg/l | +
The data is added to the physico-chemical template and checked for accuracy in the same way that biodiversity occurrence data are checked prior to uploading. To ensure that data are accurate, several steps should be taken before uploading physico-chemical data. After consolidating the physico-chemical data in the data file, you should check the following:
+Apply filters for checking the data by highlighting the header row, clicking Data, Filter
+
UUID. This is a unique if for each occurrence record. It needs to be copied and pasted so that the formula used to generate it is saved as a number. See below for guidance. https://docs.rbis.kartoza.com/batch-importing-taxon-occurrence-data-bims/dealing-unique-identifiers/
+The UUID formula is available here:
+=LOWER(CONCATENATE(DEC2HEX(RANDBETWEEN(0,POWER(16,8)),8),"-",DEC2HEX(RANDBETWEEN(0,POWER(16,4)),4),"-","4",
+DEC2HEX(RANDBETWEEN(0,POWER(16,3)),3),"-",DEC2HEX(RANDBETWEEN(8,11)),DEC2HEX(RANDBETWEEN(0,POWER(16,3)),3),
+"-",DEC2HEX(RANDBETWEEN(0,POWER(16,8)),8),DEC2HEX(RANDBETWEEN(0,POWER(16,4)),4)))
+Systematically check each column using the dropdown arrows, and look for inconsistencies. Some common issues include, #num in UUID column instead of the UUID, incorrect spelling in the Site description column (e.g. Gakiriro wetland, Gakirirowetland), latitude with missing “-“ (e.g. 2.60059 as latitude is incorrect – should be -2.60059), longitude.
+Also check that all sites fall within the country boundary so that Site Codes may be generated correctly and geocontext data harvested for each site.
+
+
Check Sampling date is in the correct format : yyyy/mm/dd
+Check that all Chem codes are correct and are present in the Chemistry units table. New variables can be added. See Managing BIMS Admin tables – Chemistry tables.
+
Check that all variables have been converted to their correct unit of measurement.
+Check Collector/Owner and Collector/Owner Institute. Ideally CAPITALS should not be used, First name Surname if known. Do not use middle initial and punctuation.
+
Check the metadata (Author(s), Year, Source, Title, Reference category, URL, DOI, Document Upload Link). For each study reference type, you need to populate the following columns:
+Check format of Author(s). It needs to be: Surname + Initials, no punctuation. (e.g. Tumushimire L, Mindje M, Sinsch U & Dehling JM not Lambert Tumushimire, Mapendo MINDJE, Prof. Ulrich Sinsch & Julian Maxmillian Dehling). It is important to get the authors correct (e.g. Sinsch Ulrich and Dehling, J. Maximilian, Lümkemann Katrin, Rosar Katharina, Christiane Schwarz should be Sinsch U, Lümkemann K, Rosar K, Schwarz C & Dehling M as per the doi).
+
Check the Date: This is the publication date (so 2012-2013 should be 2019 as this is when the article was published - Ecology and Evolution. 2019. Same with all other data from this study).
+
Check the Source. Please note when to include source or not, and what to include. (e.g. Mindje, M., Tumushimire, L., & Sinsch, U. (2020). Diversity assessment of anurans in the Mugesera wetland (eastern Rwanda): impact of habitat disturbance and partial recovery. Salamandra, 56, 27-38. Should be Salamandra)
+
Check the Title. For Peer-reviewed scientific article the Title is the title of the article, for Published reports or theses, it is the title of the thesis. Unpublished data don’t need a title.
+
Check all Reference Categories are correct: options include:
+
Check URL and DOI. Use a DOI if it is available, URL – only needed for Peer-reviewed scientific article if there is no DOI. For the DOI you only need to include the number part, so 10.1080/15627020.2012.11407524, not https://doi.org/10.1080/15627020.2012.11407524.
+
+
Check the document upload link is correct. Note the Document Upload Link is obtained after the report is added. Reports are only uploaded when there is no DOI or URL to link the data to.
+Checking for duplicate occurrence records. Use this formula for checking for duplicates. This is a combination of Site description, latitude, longitude, sampling date, Chem code, author, year, source and title. Copy and paste the formula below into a new column at the end and name it “Duplicate check”.
+ +Then copy and paste the formula down to the end of the data rows. Then Highlight the column, and from the Home menu, select Conditional Formatting, Highlight Cells Rules, Duplicate Values.
+
Any duplicates will be highlighted. Check and delete duplicate occurrence records. Then delete the Duplicate Check column.
+Delete blank rows and columns. Lastly, ensure that there are no extra blank rows or columns, by deleting them.
+
Remove the data filter, save the file in excel, and save the file as csv file.
+
Go to Profile – Upload Physico-chemical data
+
This opens the Upload Physical Chemical Data form. Browse to the correct file and click upload.
+
On completion the following success file is shown.
+
This section explains how an administrator or user adds a site and data to a site.
+An administrator or user can add a new site using the Add Site button on the menu bar.
+
This opens the Add a Location Site form:
+
The user then adds the latitude and longitude by inserting the co-ordinates or clicking on correct location on the map, click Generate Site Code. This is automated and includes the Catchment + Province ID +District ID + Site count.
+
An original site code can also be added if this was included in the source reference, as well as a description of the site. The owner is specified using the dropdown if the logged in user is not the owner. Site images can be added. Lastly, the user agrees to these data being shared via the RBIS platform for visualisation and download by registered RBIS users, and click Add. The new site is thus created.
+New occurrence data can be added from both the site form and by using the + Add on the side panel.
+
Clicking Add on either, opens the data capture form for a specific biodiversity module. The administrator or user needs to add the Date, specify the owner, and select the broad biotope, specific biotope, substratum, sampling method, sampling effort and record type using the relevant dropdowns. Note that only options specified in the Administrations tables are available for selection here (see separate documentation on Managing BIMS Admin tables). If this information is not available then it is left blank. A site image can be added.
+
Occurrence data is then added. The taxa included in the form include all taxa recorded within a 25km radius of the site as a default. The user then needs to check the box, and add a number recorded. If abundance has not been recorded then this is left blank. The user can add abundance as number, percentage abundance and density (m2) by changing the selection in the Abundance dropdown.
+
If the species observed is not shown in the default list, then the user can click Add Taxon, which links to the master list for the taxon group, or Add New Taxon, which open GBIF and allows the administrator or user to select a species in GBIF. After completion of the data, the user agrees to these data being shared via the RBIS platform for visualisation and download by registered RBIS users, and clicks Next, and Submit.
+
This opens the Abiotic form, which is populated using the dropdowns, check boxes and value fields. If no abiotic or physico-chemical data have been recorded then these fields are left blank. Units for measurement are specified for each and the user needs to convert their physico-chemical data to the correct unit before adding values. After completion of the data, the user agrees to these data being shared via the RBIS platform for visualisation and download by registered RBIS users, and clicks Next, and Submit.
+
The last form is for adding the Source Reference
+
Then confirm Submit
+
A specific administration module has been developed to allow administrators to manage taxa within the information system. The taxa shown in Taxon Management are those taxa that have been uploaded via the “Upload Taxonomic Data”.
+
Only registered users with super user status are able to access Taxon Administration, typically the administrators .
+The name of the Taxon Group and logo can be updated easily by highlighting the group, and clicking “Edit”, then typing the new name in “Label”, and browsing to the correct logo.
+
The taxon is then shown:
+
Click “Edit” to open up a pop up, which allows you to edit the details of a taxon.
+
Several fields (indicated with a red arrow) can be edited and changed if they are incorrect including, GBIF Key, Scientific Name, Canonical Name, Legacy Canonical Name, Taxonomic Rank, Vernacular or common name, Taxonomic status, Parent taxon, National Conservation Status (SANBI Red Listing), Global Conservation Status (IUCN Red Listing), Endemism and Origin. Most of these are auto-populated when a taxon is uploaded using the Master List or added as a new Taxon in Taxon Management.
+
Click the “GBIF” to link to the species on GBIF:
+
Click the “GBIF” to link to the species on GBIF:
+
If a new taxon needs to be added to the group, click the “Add a Taxon” button, type in the species name, and click “Find”.
+
If the Taxon is on GBIF it will provide the link to the GBIF taxonomic backbone, then click “Add” to confirm the addition of the new taxon to the taxon group.
+
If the taxon is not on GBIF, the administrator may add the new taxon, after which they must assign it to the appropriate Family and indicate the taxonomic rank. Note only genus and or species may be added.
+
Then edit details of the taxon by following the 36.1.5 Checking and/or changing a taxon’s origin, endemism, conservation status and common name process.
+This needs to be used with caution. If data are associated with the taxon, then you will not be able to delete the taxon.
+
Click on the magnifying glass symbol, to return the records associated with a specific taxon.
+
Click on the CSV button to download the CSV file of all taxa within a taxon group, or the subset of taxa selected using the filters.
+
These can then be viewed in excel.
+
By default images of a taxon are harvested from GBIF is they exists. In some instances an administrator may want to add images of a taxon themselves. To do this:
+
It may be desirable to add attributes for specific taxon groups such as “Water dependence” (Highly dependent, Moderately dependent, Minimally dependent, Terrestrial). These additional attributes are assigned to each taxon during the uploading of the master lists as long as the additional attribute is added in Taxon Management before uploading. +This is done in the Edit Module form, Add attribute. The attribute needs to match the attribute column header in your Master List for uploading.
+
You can add taxon specific attributes to a taxon group by adding additional column to the Master list and uploading , or individually by adding to the “Change Taxonomy” form:
+Only registered users with super user status are able to do this, typically the administrators.
+Click on your name and select Upload Taxonomic Data
+
Click Add new – to add a new Taxon Group
+
Add the new taxon group by adding the Taxon Group name and selecting the logo using the “Browse”
+
Select the new Taxon Group using the dropdown and browse to the file containing the Master List of Taxa for the Taxon Group, click upload.
+
++Note: The Excel file needs to be saved as a csv using the following option:
+
Progress is shown:
+
A Success File will indicate taxa uploaded to the system. An Error file will give details of taxa not uploaded. The last column in this csv file provides an indication of the reason the taxon was not uploaded. The administrator then needs to check the data and correct before uploading again.
+
Once the Master List of Taxa has been added it can be viewed in the Taxon Management section. +An Error File provides details of the problem in the last column of the csv. Once these have been corrected, the file can be uploaded again.
+
New taxa may be added individually using the Taxon Management, or if there are multiple new taxa to be added, then the steps can be repeated, to upload the additional new taxa for the Taxon Group.
This section explains the process when a user adds data to RBIS, and how the administrator views, checks and validates the occurrence record or new taxon.
+Data served on the platform includes both validated and unvalidated data, where validated implies some degree of checking that the record is accurate. The user is able to select one or the other using the filter:
+
All data added to platform by administrators using the Upload Occurrence data template, is given the status of validated on the assumption that the administrator has checked the data prior to uploading.
+However, when a user adds data directly to the platform, this data remains unvalidated until the administrator checks the data.
+When a user adds new occurrence data, the data is automatically assigned an unvalidated status. The administrator is sent an email alerting them to the new record.
+
This unvalidated record is also added to the Validate Records form, which the administrator has access to.
+
This form includes functionality to See Unvalidated data, and filter by Owner, Site Code, Source Collection or Module. The administrator can then undertake the following actions, using these buttons
+
Viewing: the data is viewed by the administrator and checked for accuracy in terms of all entries including the taxa recorded. If a taxon is outside of its expected geographical range, then the administrator would reject the data with a reason to the person who uploaded the data.
+Reject: the data is rejected and the user receives an email notification with the reason. The user then has the opportunity to edit their data and resubmit for validation.
+Validate: the data is validated by the administrator if everything is correct.
+Delete: this is only used when data have been accidentally added to a site but is generally easier done via the data forms.
+Generally a user should not need to add a new taxon often as the master lists for each biodiversity module are updated and represent the full expected checklist of species for a country. However, in the event that the user records a new taxon not currently in the master list, they are able to add this taxon to the information system. This new taxon then goes through a validation process by the administrator, and the new taxon is either accepted or rejected (with reasons).
+The administrator receives a message alerting them to a new taxon that has been added. They then follow the link and validate the taxon, then accepting or rejecting it with reasons, which are provided by email to the user who uploaded the new taxon.
+
Follow the link to Taxon Management:
+
Check the taxon, and if it is acceptable to add to the Master List, then click Validate. Note the administrators may need to seek expert taxonomic input. The user receives an email indicating that the data has been approved.
+If it is not acceptable, the Reject the taxon. An email will be sent to the user who uploaded the records, with reasons for the rejection.
+Note: A new occurrence record (site visit) cannot be validated if the new taxon has not been validated. On Validate records it is shown as an Unvalidated taxon. First the administrator must validate the taxon by following the link in the email, or by clicking on the Validate Taxon button below. The taxon is then either validated or rejected. Once the new taxon has been validated, then the record can be validated.
+Before the taxon is validated:
After the taxon is validated:
+
This guide will help you display images inline, just like the one below:
+
Start by navigating to the section editor on the landing page. Once there, create a new section.
+To facilitate the upcoming steps, switch the editor to full-screen mode. Click on 'maximize' to do this.
+
To switch to the next column, simply press the 'Tab' key on your keyboard.
+
Click on 'Maximize' once more to exit the full-screen mode. Click 'Save' to preserve your changes.
+Verify that the newly created landing page section has been added to the current theme. This will ensure your changes are visible on the landing page.
+
This guide will help you in adding a new section to your landing page.
+
(1) Name the new section (note that this name will not appear on the landing page).
+(2) Optionally, add a title that will be displayed on the landing page.
+(3) Set the background color for the section.
+
Click 'Save and continue editing'. This will allow you to add content to the section afterwards.
+If you have previously created landing page section content, you can select it in the content field. If not, you can add a new one by clicking the plus button.
+Once you have finished editing the new content, click 'Save'. Remember, you can always update this later.
+
Click 'Save'. The next step is to add this section to your theme. Navigate to 'Custom Themes' and select the enabled theme.
+Scroll to 'Landing page sections' and select your new section. If you want to select more than one section, hold down the Control key (or Command on a Mac).
+
Click the 'Copy' button on the bottom right. This action copies the video's embed code to your clipboard
+
In this article we explain the concept of the GeoContext platform and how layers are published to it in BIMS.
+
A GeoContext collection is a set up web map services that can be queried in order to discover habitat or other relevant spatial data for a site.
+
From GeoContext collection admin page click Add collection button to create a new collection
+
Fill out the required fields :
+Click Save when you're done
+A GeoContext group is a subset of layers from a GeoContext collection that form a logical group, usually based around a theme such as temperature, political regions etc.
+
You can arrange the group order as follows:
+In order to remove group from the group just click the x sign
+
You can create a new group from the context group page or directly from layer admin page.
+In order to create new group you need to fill out the required fields:
+See other existing groups for guidance.
+In this sectio we describe how you add a layer to a GeoContext group. A layer is a Web Mapping Service intended to make spatial information available over the internet, covering a specific thematic topic e.g. average annual temperature in March
+
You can arrange the layer order as follows:
+In order to remove layer from the group just click the x sign
+
Click Save when you're done updating the group.
+You can create a new layer from the context group page or directly from layer admin page.
+In order to create new layer you need to fill out the required fields:
+{geoserver_host}/geoserver/wfsSee other existing layers for guidance.
In this section we explain the process of configuring BIMS to harvest GeoContext data from a GeoContext server for a collection of layers.
+
This section describes how to configure your geocontext settings to harvest GeoContext data for each site.
+
Open geocontext settings in admin page +Find Geocontext group keys field
+
++Make sure that the key exists in the GeoContext, to check you can use this api :
+https://staging.geocontext.kartoza.com/api/v1/geocontext/value/group/1/1/{geocontext_key}/and change the geocontext_key in the url with the key you want to check
In this section we explain how to create a location context group in the django admin interface for BIMS.
+
)
To create a Location Context Group in BIMS, you need to know what layers are returned from the GeoContext group.
+For instance, we want to create Location Context Group for Rwanda Catchments.
+First, check the output from GeoContext with this API : +https://staging.geocontext.kartoza.com/api/v2/query?registry=group&key=river_catchment_areas_group&x=24&y=-29&outformat=json
+Note : Change river_catchment_areas_group in the url with GeoContext group you want to add.
+You will receive this data from GeoContext :
+
There are two service registry values (layers), so you need to add them both to the Location Context Group to display all those layers in the filter.
+To add those layers please follow these steps :
+Note : We will use this data for the following steps
+
Then you need to do the same thing for other layer.
+
If you've done it correctly, then you will have two new layers in Location Context Group admin page :
+
In this section we explain how to create a Location Context Filter in BIMS.
+
Location context filter is just the filter name for the spatial filter on the Map page.
+
To add groups (Rwanda Catchments Level 1 & Rwanda Catchment Level 2) to the Location context filter please follow this guide.
+To add new Location context filter please follow these steps :
+Save when you've doneIn this section we describe the process of sorting Location Context Groups to control the order in which they appear in BIMS.
+
To do this guide, you need to add Location Context Group and Location Context Group Filter beforehand.
+Open the admin page for Location Context Filter Group Order +Click Add location context group order button at the top right +Fill up these fields :
+Group - Choose Location Context Group you want to show in the filter panel
+
Filter - Choose Location Filter you want to show in the filter panel
+
Group display order - This is the order of the groups inside the location filter
+
Show in dashboard (optional) - Whether to show this data in the dashboard or not
+
Show in side panel (optional) - Whether to show this data in the side panel or not
+
Click Save when you've done.
+In this article we describe the process of updating the GeoContext data in one or more sites using the admin panel.
+
To update GeoContext data for existing sites please follow these steps :
+
This subsection describes how to publish layers as WMS (Web Mapping Services) for use by GeoContext or as Visualisation layers. BIMS deploys with an instance of GeoNode that can be used for publishing these layers, but you can use any standards compliant web mapping server for this purpose.
+
First let us define the terms 'GeoContext Layer' and 'Visualisation Layer':
+GeoContext layers are layers that you publish online as an OGC web service with the explicit intention that these layers are harvested by the https://staging.geocontext.kartoza.com GeoContext service.
+Visualisation layers are used in the layer selector in BIMS and allow the user to add map overlays in the BIMS map view - for example to show soil types or catchment boundaries on the map.
+In the next steps we will show you how to publish both of these types of layers.
+This article gives a short explanation of how to publish a layer in GeoNode. This is one way to provide a layer in GeoContext yourself.
+
To publish a layer from GeoNode you can follow this guide : https://docs.geonode.org/en/master/usage/managing_layers/uploading_layers.html
+The guide shows you how to add metadata to the layer you have published.
+
To add metadata to the layer in GeoNode please follow this guide : https://docs.geonode.org/en/master/usage/managing_layers/layer_metadata.html.
+In this guide we show you how to find out the WMS URL for a published layer so that the layer can be published in GeoContext or as a GeoContext layer.
+
Discovering the WMS URL for a map service requires that you have a platform where you can browse the services. This could be done though a GIS client such as QGIS or on a web interface such as GeoNode or GeoServer. For this example we will show you the workflow in GeoNode.
+First browse to the map layer in GeoNode that you want to publish in BIMS:
+
Next click on the metadata detail button to view the metadata for the layer.
+
On the metadata page you will see a long list of information about the layer. First make a note of the "Title" of the layer e.g.:
+++LULC_2018_
+
Now scroll down until you find the section called "References" and then look for the heading "OGC WMS: geonode Service". Right click on the service link and choose "Copy link location" from your browser's context menu.
+Save the service URL that is now in your clipboard e.g.:
+https://geonode.rbis.kartoza.com/geoserver/ows
+In this guide we will show you how to publish a non-biodiversity layer in FBIS. Non-biodiversity layers can be displayed on top of the base map in FBIS to provide insights about the spatial situation of collection sites.
+
In order to add a layer to the FBIS, follow these steps :
+
These layers will appear in the Layer Selector on the map page.
+
In this guide we will explain the high level concepts of the GeoContext subsystem which is used to derive location related data for each occurrence record added to RBIS.
+GeoContext is an independent service, available at https://geocontext.kartoza.com/. The purpose of GeoContext is to harvest data for point locations from a range of online databases. GeoContext allows you to register WMS/WFS/WCS layers in groups which in turn can be registered in a collection. You can then pass it a point locality and it will query every layer in the collection, returning a set of values, one for each layer under the point location.
+
As you can see from the above diagram, the workflow consist of three parts:
+1) Publishing layers under e.g. WMS
+2) Registering layers, groups and collections in the GeoContext service
+3) Registering the GeoContext service(s) with BIMS
+This tutorial will lead you through all of these steps. We expect that you are already familiar with platforms such as GeoNode, GeoServer and concepts such as OGC services. We also expect that you are familiar with and understand the basic operations and management of BIMS.
+The following YouTube video walks through the steps described in this section of the documentation in detail with examples. If you are viewing this as a PDF or on the web, you can click on the image below to open the YouTube video.
+
This document guides users through the process of publishing spatial data (from a PostgreSQL database or raster data) in GeoServer and how to do basic cartography. This training material is broken up into the following sections:
+Spatial data consist of vector and raster data. In this guide we will explain the +process of loading vector data into a PostgreSQL database.
+++We assume users have a running instance of QGIS on their machines. If you +do not have a running version you can download and install an appropriate QGIS version based on your architecture. Also acquire the credentials for the database from your database administrator.
+
There are various ways to load vector data into the database but, we will concentrate +on the easier methods. This usually involves the following:
+Step 1. Open QGIS Desktop.
+Step 2. On your icons toolbar click the PostgreSQL icon to add layer or alternatively click on the Layers Menu > Data Source Manager > PostgreSQL 
Step 3. Click to create a new database connection. 
Step 4. Populate the dialogue with your user credentials. 
Step 5. Save your connection parameters.
+All panels in QGIS can be docked and arranged based per user's needs. It is +encouraged to dock your layers and browser panel on opposite sides in QGIS.
+
Step 1. Load your vector layers into QGIS.
+Step 2. Open the browser tab that you have docked on the opposite end of the layer panel.
+Step 3. In the browser panel navigate to open the PostgreSQL connection you defined
+earlier on.
+
+Step 4. Select the appropriate schema from your PostgreSQL connection.
+Step 5. Drag the layer from the layers panel dropping it onto the selected schema
+in the browser panel.
+Step 6. Wait for the layer to complete loading.
After loading the layer it will be available in the selected schema and ready to use in GeoServer.
+When using this method it is assumed a user has already defined a database connection.
+Step 1. Navigate to the Database Menu in QGIS and from the drop down choose
+DBManager. Database Menu > DB Manager
+
+Step 2. Select your PostgreSQL connection.
+Step 3. Click on the Import Layer/File on top of the DB Manager dialogue.
+Step 4. Populate the import layer dialogue choosing the appropriate options.
+
+Step 5. Accept the values and wait for the layer to be loaded.
+The QGIS processing tool also provides other options to load spatial +data into a PostgreSQL database. Those tools also provide the users with the option +to do bulk inserts of multi layers simultaneously.
+
GeoServer is a Java based open source software server which has the ability to share and edit geospatial data in open standard format. GeoServer allows a user to add, remove, edit and control geospatial content through a web browser, which can generate different OGC standard services such as WMS, WCS, WFS, and SLD etc. The main objective and purpose of GeoServer is to offer potential to create maps and share data in compliance with OGC standards.
+The diagram below shows the workflow relating to ingesting data into GeoServer and previewing the data.
+
Content above available from learning geoserver.
GeoServer can publish vector data from various sources i.e shapefile, geopackage. In our +use case we already have spatial data stored in a relational database and, we will be publishing this data to GeoServer. A relational database has a lot of advantages over the traditional formats i.e shapefile hence our preference to load the data into the database firstly.
+The process of publishing vector data in GeoServer involves the following steps:
+Since the GeoServer we are using in being used in production we have already defined the first two steps (for vector data) and will not be focusing on them here. For Raster data +we will be defining step 2 and step 3 for the publishing work-flow.
+Step 1. Login to the Geoserver instance i.e Local GeoServer using the credentials that have been shared with you.
+Step 2. Click on the layer menu option A on the image below.
+
Step 3. Click on option B shown on the image above.
+Step 4. Choose a store you want to publish the layer from. This should be the sanbigis store.
+
Step 5. Select the appropriate layer you wish to publish.
+Step 6. On the Data tab edit the following properties.
+
to the publishing tab:
| Property | +Description | +
|---|---|
| Name | +name this will be identified with | +
| Title | +Friendly name | +
| Abstract | +Add short description about the layer | +
| Bounding Boxes | +choose compute from data and compute from native bounds | +
Then select an appropriate style to use with your layer.
+
Step 7. Save your changes and your layer will be visible within GeoServer.
+In order to publish raster data, you will need to upload the files onto the server +where your GeoServer instance is hosted. This is usually done by the Administrator +or you can do it yourself if the Resource Browser plugin is installed.
+Step 1. Make sure the layers you need to publish are already stored on a folder visible within GeoServer data directory.
+Step 2. Click on Stores in the Data side menu.
+Step 3. Add a new store selecting the appropriate raster data type. The preferred format is Geotiff.
+
Step 4. Fill in the raster dialogue as depicted below:
+
Step 5. Save the values in the dialogue and proceed to publish the layer.
+Step 6. On the Data tab edit the following properties.
+| Property | +Description | +
|---|---|
| Name | +name this will be identified with | +
| Title | +Friendly name | +
| Abstract | +Add short description about the layer | +
Step 7. On the publishing tab choose the appropriate style and the layer will be visible in GeoServer.
GeoServer provides a couple of ways to symbolize vector and raster data. The most +common way is by using SLD (Styled Layer Descriptor) which is an OGC standard. +GeoServer also adds some flavour to the format which enriches how to symbolize vector/raster +data. Other less common ways to symbolize data include using CSS(Cascading style sheets) and YSLD.
+There are various open source software which allows you to export SLD natively. Since we are +familiar with QGIS we will use it as our de facto Desktop GIS system.
+++Although QGIS can export SLD it does not produce a 1-1 mapping of the rich +cartography that is available in QGIS. It is recommended to use simple styles when your goal +is to use the SLD exporter from QGIS.
+
Step 1. Load your vector layers in QGIS.
+Step 2. Right-click on the vector layer and choose the symbology tab.
+
Step 3. Select an appropriate style from the options. Be thoughtful of all the +cartographic rules and the limitations of the exporter when choosing a style.
+Step 4. If you are satisfied with your result click Apply.
+Step 5.Click on the Style link to show the hidden context menu.
+
Step 6. Save your style as SLD.
+
Step 7. Export the SLD to disk and wait to upload to GeoServer.
+Step 1. Navigate to GeoServer and click on the style tab.
+Step 2. Click to Add New Style.
+Step 3. Browse and upload your style into GeoServer.
+
Step 4. Submit your results and this will take you back to your style.
+Step 5. Use the search box at the top of the style to identify the name of the style you created above.
+
Step 6. Open the style again and indicated below.
+
Step 7. Select the layer you want to associate your style with.
+
There are two options:
+Step 8. Submit your results.
++This process applies to also styling raster data.
+
QGIS provides native ways to interact with services coming from GeoServer. +Both services are OGC compliant and can communicate using the following protocols:
+For each protocol, QGIS provides a native way to interact and authenticate against.
+Step 1. Activate the Data Source Manager.
+Step 2. Select the protocol you need to define and add a new connection.
+Step 3. Populate the dialogues. All the dialogues will have the same format.
+WMS Dialogue:
+
Step 4. Click connect to preview the resources available on the server.
+
Step 5. Select a layer to load into Geoserver and start interacting with it.
+Repeat the above procedure for each service types.
This section contains all documentation relevant to administration procedures.
+The content is divided into four sections:
+This guide will help you fetch the park name from a spatial layer on the "Add Site" form, following the steps outlined below:
+
As a superuser, navigate to the layer upload page at /upload-spatial-layer/ to upload your shapefiles. When prompted, give the layer an appropriate name based on your needs.
+
After uploading, wait until the process is completed. The upload status will change to "Success" once it's finished.
+Next, go to the admin page and select Site Setting by visiting /admin/bims/sitesetting/. Click on the first setting that appears.
+Scroll down to find the Park Layer dropdown, and choose the layer you just uploaded.
+Set the Park Attribute Key to specify the attribute you want to use when selecting park names from the layer’s properties.
+Once all these settings are configured, click Save.
+
Once all these settings are configured, click Save.
++Note: Only admin/super users can upload spatial layers.
+
Click here to access the upload spatial layers page.
+This is how it looks.
+
Name: Enter the name of the layer.
+Choose files: Select the shape file and auxiliary files to upload.
+Submit: Uploads the files.
+❎: Close the form.
+Click on the Choose files button to select the shape file and auxiliary files to upload.
This will open the file explorer from where user can select the necessary files for their layer.
+++Note: Users should select multiple files at the same to upload.
+
Cancel: Cancel the process.
+Open: After selecting the files, click on the Open button to upload the files.
✅ Open files read only: Open the files in read only mode.
+None: File extension.
+This process will take some time to complete.
+This error appears when the uploaded files exceeds the maximum size limit.
+
Indicates that the process has started.
+
Indicates that the process is in progress and may take some time to complete.
+
Indicates that the files have been uploaded successfully.
+
Users will receive a success message.
+
Indicates that the files failed to upload.
+After successfully completing the process, the user will gain access to the editor page.
+Click on the Editor button to access the editor page
This is the UI of the Editor page.
To access the admin page, hover on the Administration drop down menu from the top navigation bar.
Choose the Admin Page option from the drop down menu. This will open the admin page.
Navigate to the Cloud Native Layer section from the left menu.
Click on the Cloud Native Layer heading to navigate to this section on a new page.
Layer uploads: By clicking on this, users will be able to see all the uploaded layers.
+
1. total: Displays the total number of layers uploaded.
+2. Data: This is the list of uploaded layers with the corresponding details.
+3. Add layer upload: This button is used to upload a new layer.
+4. Filter: By using this, users can filter the data. After clicking on this a dropdown menu will appear.
+
Layer: This is used to filter the layers by name.
+Status: This filter allows users to arrange the layers by their current status such as success, failed, etc.
+
5. Dropdown menu: This menu allows users to perform some actions on the data. This are the available options.
+
Import data: This option allows users to import the data.
+Delete selected layer uploads: This option is used to delete the selected layers. Users can delete multiple layers at once.
+6. Go: This button allows users to proceed with the actions they have selected from the dropdown menu.
+Layers: By clicking on this users will be able to see the list of the layers they have uploaded including their details.
+
1. total: Total number of layers.
+2. Data: This is the list of layers with their details such as id, status, created_by, etc.
+3. Add layer: This button allows users to upload a new layer from the admin panel.
+4. Dropdown menu: This menu allows users to perform some actions on the data. This are the available options.
+
Delete selected layers: This option is used to delete the selected layers. Users can delete multiple layers at once.
+Go: This button allows users to proceed with the actions they have selected from the dropdown menu.
+