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Joaquim Santos studied Biology at the University of Coimbra, graduating in 2003. With a background in Ecology, his work focuses on Biological Collections and Biodiversity Data, particularly their digitisation, integration, and reuse in research and society. He has been actively involved in several initiatives, including the Digitization of the Herbarium of the University of Coimbra, the Digitization of the Botany Library and Archive, and the development of digital infrastructures such as the eHALOPH platform (a database dedicated to halophytes). In 2018, he completed his Master’s in Ecology with the dissertation “Accelerating Digitization of Biological Collections for Fast Ecological Information Retrieval”, which led to the creation of EXPLORATOR, a crowdsourcing platform supporting the digitisation of biological collections. His current interests include Open Science, Linked Open Data, and semantic technologies, exploring how knowledge graphs, standards, and interoperable data infrastructures can enhance the accessibility, visibility, and impact of biodiversity information. He has contributed to Portuguese and international initiatives in Biodiversity Data and Digitisation, promoting more open, connected, and reusable scientific data ecosystems.
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Identification

Personal identification

Full name
Joaquim Santos
Date of birth
1978/01/11
Gender
Male

Citation names

  • Santos, Joaquim

Author identifiers

Ciência ID
0D1D-7A7A-A97C
ORCID iD
0000-0002-2160-4968

Email addresses

  • joaquimsantos@gmail.com (Personal)

Addresses

  • Centro de Neurociências e Biologia Celular (CNC-UC), Rua Larga, 3004-504, Coimbra, Coimbra, Portugal (Professional)

Knowledge fields

  • Natural sciences - Biological Sciences - Ecology

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
English Intermediate (B1) Intermediate (B1) Intermediate (B1) Intermediate (B1)
French Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1)
Spanish; Castilian Intermediate (B1) Intermediate (B1) Intermediate (B1) Intermediate (B1)
Education
Degree Classification
2006
Concluded
 Ecologia (Mestrado integrado)
Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal
 Em fase de conclusao
2003
Concluded
 Biologia (Licenciatura)
Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal
 15
Affiliation

Science

Category
Host institution		 Employer
2025/09/15 - Current Science and Technology Management Universidade de Coimbra, Portugal
2018/11/27 - 2025/09/14 Science and Technology Management Universidade de Coimbra Centre for Functional Ecology - Science for People & the Planet, Portugal
Projects

Grant

Designation Funders
2013/07 - 2015/11 INVAsive plant species management in Portugal: from early DEtection to Remote sensing and Biocontrol of Acacia longifolia - INVADER-B
Provided by PTCRIS: 131547
 Fundação para a Ciência e a Tecnologia, I.P.

Contract

Designation Funders
2019/01/01 - 2019/12/31 Centre for Functional Ecology
UID/BIA/04004/2019
Universidade de Coimbra Centre for Functional Ecology - Science for People & the Planet, Portugal

Universidade de Coimbra, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2013/07/01 - 2015/11/30 Gestão de plantas INVasoras em Portugal: da prevenção à DEtecção Remota e controlo biológico de Acacia longifolia - INVADER-B
PTDC/AAG-REC/4607/2012
Instituto Politécnico de Coimbra, Portugal

Universidade de Coimbra Centre for Functional Ecology - Science for People & the Planet, Portugal

Universidade de Coimbra, Portugal

Instituto Politécnico de Coimbra Centro de Estudos de Recursos Naturais Ambiente e Sociedade, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2011/01/01 - 2013/12/31 Projecto Estratégico - UI 239 - 2011-2012
PEst-OE/AGR/UI0239/2011
PEst-OE/BIA/UI4004/2011
Universidade de Lisboa Instituto Superior de Agronomia, Portugal

Universidade de Coimbra Centre for Functional Ecology - Science for People & the Planet, Portugal

Universidade de Coimbra, Portugal

Universidade de Lisboa Centro de Estudos Florestais, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Book
  1. Machado, Maria; Santos, Joaquim; Covelo, Filipe. Explorator. Explorar o mundo das plantas. Portugal: Zenodo. 2021.
    10.5281/ZENODO.5910451
  2. Fátima Sales; Filipe Covelo; Joaquim Santos; Daniela Cordeiro. Colecções Biológicas. 1. Colheita de Angiospérmicas, Gimnospérmicas e Fetos. 2018.
    10.5281/zenodo.13904183
Book chapter
  1. Tavares, A. C.; Silva, S.; Santos, J.; Paiva, I; Oliveira, J.; Bettencourt, T.. "Inquire at Coimbra botanic garden: Products and process of an IBSE educative project". 4353-4356. 2014.
    10.1016/j.sbspro.2014.01.945
Conference abstract
  1. Gouveia, António; Santos, Joaquim; Silva, Ana Margarida Dias da. "The Importance of Historical Biodiversity Data Transcribed from Botanical Garden Archives: Results from the Citizen Science Project 'Plant Letters' on Zooniverse". Paper presented in DH2024, Washington, D.C., 2024.
    Published
  2. Almeida, Inês; Santos-Carvalho, Ana; Domingues, Catarina; Caliman Fontes, Lorena; Direito, Bruno; Especiosa, Maria Olímpia; Miguéis, Ana Eva; et al. Corresponding author: Almeida, Inês. "Open Science Community Coimbra: cocriação do plano mestre". Paper presented in Comunidades de Ciência Aberta na UC 2024, Coimbra, 2024.
    Published
  3. Almeida, Inês; Direito, Bruno; Caliman Fontes, Lorena; Santos, Joaquim; Miguéis, Ana Eva; Santos-Carvalho, Ana; Neves, Maria João; Noro, Jorge. "Criar uma Comunidade de Ciência Aberta: passos e desafios na Universidade de Coimbra". Paper presented in 10th Forum GDI, Setúbal, 2023.
    Published
  4. Sabine von Mering; Paul Jean-Charles Braun; Robert Cubey; Quentin J. Groom; Elspeth Haston; Annika Hendriksen; Rukaya Johaadien; et al. "Modelling Research Expeditions in Wikidata: Best Practice for Standardisation and Contextualisation". 2023.
    10.3897/biss.7.111427
Conference paper
  1. Tavares, Ana Cristina; Silva, Susana; Santos, Joaquim; Paiva, Isabel; Oliveira, João; Figueiredo, Albano; Bettencourt, Teresa. "Inquire: why teaching about the conservation of biodiversity and climate change?". Paper presented in Sixth Eurogard - European Botanic Gardens Congress, Chios, 2012.
    Published
Conference poster
  1. Joaquim Santos. "Expeditia.info". 2025.
    10.5281/zenodo.14812542
  2. Sabine von Mering; Siobhan Leachman; Joaquim Santos; Heidi Meudt. "Engaging with Wikidata: Benefits and impacts for botanists and institutions". 2024.
    10.5281/zenodo.11102529
Journal article
  1. Sabine von Mering; Siobhan Leachman; Joaquim Santos; Heidi M Meudt. "Wikidata for botanists: benefits of collaborating and sharing Linked Open Data". Annals of Botany (2025): https://doi.org/10.1093/aob/mcaf062.
    10.1093/aob/mcaf062
  2. Sérgio Timóteo; Ruben Heleno; Filipe Covelo; Joaquim Santos; Pedro Lopes; António C. Gouveia; Arménio Matos; et al. "HiDaFernPT: Historical data of spore availability for 121 fern and lycopod taxa in Portugal (1926–2013)". Ecology (2025): http://dx.doi.org/10.1002/ecy.70026.
    10.1002/ecy.70026
  3. Sabine von Mering; Robert Cubey; Dag Endresen; Annika Hendriksen; Siobhan Leachman; Daniel Mietchen; Joaquim Santos. "Advancing Community Curation of Research Expeditions: A Collaborative Journey with Wikidata and Biodiversity Information Standards". Biodiversity Information Science and Standards (2024): https://doi.org/10.3897/biss.8.138921.
    10.3897/biss.8.138921
  4. Ruben Heleno; José M. Costa; Filipe Covelo; Joaquim Santos; Pedro Lopes; António C. Gouveia; Arménio Matos; et al. "O armário: Fruiting phenology data for 4,462 plant taxa in Portugal (1926–2013)". Scientific Data (2024): https://doi.org/10.1038/s41597-024-03520-9.
    10.1038/s41597-024-03520-9
  5. Groom, Quentin; Dillen, Mathias; Addink, Wouter; Ariño, Arturo H.; Bölling, Christian; Bonnet, Pierre; Cecchi, Lorenzo; et al. "Envisaging a global infrastructure to exploit the potential of digitised collections". Biodiversity Data Journal 11 (2023): https://bdj.pensoft.net/article/109439/.
    Published • 10.3897/bdj.11.e109439
  6. Quentin J. Groom; Christian Bräuchler; Robert Cubey; Mathias Dillen; Pieter Huybrechts; Nicole Kearney; Niels Klazenga; et al. "The disambiguation of people names in biological collections". Biodiversity Data Journal 10 (2022): http://dx.doi.org/10.3897/bdj.10.e86089.
    10.3897/bdj.10.e86089
  7. Quentin Groom; Christian Bräuchler; Robert Cubey; Mathias Dillen; Pieter Huybrechts; Nicole Kearney; Siobhan Leachman; et al. "Collections do not have to Remain Ambiguous Forever: Seven steps to getting the correct people into your data". Biodiversity Information Science and Standards (2022): https://doi.org/10.3897/biss.6.91194.
    10.3897/biss.6.91194
  8. Mathias Dillen; Elspeth Haston; Nicole Kearney; Deborah L Paul; Joaquim Santos; David Shorthouse; Alison Vaughan; Sabine von Mering; Quentin Groom. "Is Your Collection Ambiguous?". Biodiversity Information Science and Standards (2021): https://doi.org/10.3897/biss.5.73702.
    10.3897/biss.5.73702
  9. Santos, Joaquim; Covelo, Filipe; Cidália Fidalgo; Machado, Maria. "Coleções biológicas". Revista de Ciência Elementar 9 1 (2021): http://dx.doi.org/10.24927/rce2021.008.
    10.24927/rce2021.008
  10. Joaquim Santos; Paulo Rupino da Cunha; Fátima Sales. "A strategy to digitise natural history collections with limited resources". Biodiversity Data Journal (2020): https://doi.org/10.3897/BDJ.8.e55959.
    10.3897/BDJ.8.e55959
  11. Marcer, A.; Haston, E.; Groom, Q.; Ariño, A.H.; Chapman, A.D.; Bakken, T.; Braun, P.; et al. "Quality issues in georeferencing: From physical collections to digital data repositories for ecological research". Diversity and Distributions (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85097029185&partnerID=MN8TOARS.
    10.1111/ddi.13208
  12. Kattge, Jens; Boenisch, Gerhard; Diaz, Sandra; Lavorel, Sandra; Prentice, Iain Colin; Leadley, Paul; Tautenhahn, Susanne; et al. "TRY plant trait database - enhanced coverage and open access". Global Change Biology 26 1 (2020): 119-188. https://publons.com/publon/28559850/.
    10.1111/GCB.14904
  13. Santos, Joaquim; Fátima Sales; Paulo Rupino da Cunha. "Accelerating Digitisation of Biological Collections: the Coimbra Herbarium case study". Biodiversity Information Science and Standards 3 (2019): https://doi.org/10.3897/biss.3.37760.
    10.3897/biss.3.37760
  14. Santos, J.; Al-Azzawi, M.; Aronson, J.; Flowers, T.J.. "EHALOPH a database of salt-tolerant plants: Helping put halophytes to work". Plant and Cell Physiology 57 1 (2016): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000373118900010&KeyUID=WOS:000373118900010.
    10.1093/pcp/pcv155
  15. Mendes, S.M.; Santos, J.; Freitas, H.; Sousa, J.P.. "Assessing the impact of understory vegetation cut on soil epigeic macrofauna from a cork-oak Montado in South Portugal". Agroforestry Systems 82 2 (2011): 139-148. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000290162300005&KeyUID=WOS:000290162300005.
    10.1007/s10457-010-9358-z
Report
  1. Siobhan Leachman; Heidi Meudt; Sabine von Mering; Joaquim Santos. 2024. Report on WikiProject International Botanical Congress 2024.
    10.5281/zenodo.13788265
  2. Arnald Marcer; Santos, Joaquim; Austin Mast; Gil Nelson; Elizabeth Ellwood; Elspeth Haston. 2023. Natural History Collections Imaging Survey Report. Current imaging practices across institutions worldwide..
    10.5281/zenodo.7837354
Thesis / Dissertation
  1. "Accelerating Digitisation of Biological Collections for Fast Ecological Information Retrieval". Master, Universidade de Coimbra, 2018. https://hdl.handle.net/10316/86223.
Website
  1. F. Sales; Santos, Joaquim. The Herbarium of the University of Coimbra. 2005. https://www.uc.pt/en/herbario_digital.

Other

Dataset
  1. Joaquim Santos; Santos, Joaquim. Natural history specimens collected and/or identified and deposited..
    10.5281/zenodo.8030869
  2. Heleno, Ruben; Costa, José M.; Covelo, Filipe; Santos, Joaquim; Gouveia, António; Girão da Cruz, M. Teresa; Timóteo, Sérgio. Fruiting phenology data for 4,462 spontaneous and cultivated plant taxa in Portugal (1926 - 2013).. 2024.
    https://doi.org/10.15468/5hymfe
  3. Ruben H. Heleno; José Costa; Filipe Covelo; Joaquim Santos; Sérgio Timóteo. <b>Fruiting phenology data for 4,462 spontaneous and cultivated plant taxa in Portugal (1926</b> <b>– 2013)</b>. 2024.
    10.6084/m9.figshare.25016432.v1
  4. Ruben H. Heleno; José Costa; Filipe Covelo; Joaquim Santos; Pedro Brito Lopes; António Carmo Gouveia; Arménio Matos; et al. Historical data of spore availability for 109 spontaneous and cultivated ferns and lycopods taxa in Portugal (1926 – 2013). 2024.
    10.15468/6gp2ha
  5. Ruben H. Heleno; José Costa; Filipe Covelo; Joaquim Santos; Pedro Lopes; António Gouveia; Arménio Matos; et al. <b>Support data for "O armário: Fruiting phenology data for 4,462 spontaneous and cultivated plant taxa in Portugal (1926 </b><b>– 2013)"</b>. 2024.
    10.6084/m9.figshare.25016432
  6. Ruben H. Heleno; José Costa; Filipe Covelo; Joaquim Santos; Pedro Brito Lopes; António Carmo Gouveia; Arménio Matos; et al. O armário: Fruiting phenology data for 4,462 plant taxa in Portugal (1926 – 2013). 2024.
    10.15468/5hymfe
  7. Ruben H. Heleno; José Costa; Filipe Covelo; Joaquim Santos; Pedro Lopes; António Gouveia; Arménio Matos; et al. <b>O armário: Fruiting phenology data for 4,462 spontaneous and cultivated plant taxa in Portugal (1926 </b><b>– 2013)</b>. 2024.
    10.6084/m9.figshare.25016432.v5
Other output
  1. Data Re-Use - Doing Research without going to the wet lab. 2025. Joaquim Santos.
    10.5281/zenodo.17552943
  2. Hands-On session: Depositing Data in Repositories. 2025. Joaquim Santos.
    10.5281/zenodo.17553184
  3. O herbário da Universidade de Coimbra na Wikidata. 2025. Joaquim Santos.
    10.5281/zenodo.15609569
  4. Integração de identificadores Wikidata para o aumento de FAIRness dos datasets. 2024. Joaquim Santos.
    10.5281/zenodo.14224840
  5. Zenodo: Funcionalidades como repositório aberto para depósito de recursos. 2024. Joaquim Santos.
    10.5281/zenodo.14046823
  6. Repositórios de dados: caso de estudo do COI Catalogue. 2024. Joaquim Santos.
    10.5281/zenodo.13753323
  7. Final follow-up workshop: Upskilling in Wikidata for maximum impact. 2024. Siobhan Leachman; Heidi Meudt; Sabine von Mering; Joaquim Santos.
    10.5281/zenodo.13384709
  8. In-person workshop Upskilling in Wikidata for maximum impact IBC 2024. 2024. S Leachman; Heidi Meudt; Sabine von Mering; Joaquim Santos.
    10.5281/zenodo.13363825
  9. WikiProject International Botanical Congress 2024. 2024. Siobhan Leachman; Sabine von Mering; Heidi Meudt; Joaquim Santos.
    10.5281/zenodo.13254276
  10. Online workshop Upskilling in Wikidata for maximum impact IBC 2024. 2024. Siobhan Leachman; Heidi Meudt; Sabine von Mering; Joaquim Santos.
    10.5281/zenodo.12741075
  11. Who is Who in Natural History Collections?. 2023. Sofie Meeus; Arturo H. Ariño; Torkild Bakken; Paul Jean-Charles BRAUN; Mathias Dillen; Dag Endresen; Elspeth Haston; et al.
    10.5281/zenodo.7781753
Activities

Event organisation

Event name
Type of event (Role)		 Institution / Organization
2021/09/08 - 2021/09/10 Workshop on Machine learning on images of natural history collections , Coimbra, 8-10 September 2021 (2021/09/08 - 2021/09/10)
Workshop (Co-organisor)
 Universidade de Coimbra, Portugal