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Joaquim Santos studied Biology at the University of Coimbra, where he graduated in 2003. With a background in Ecology, his interest are Biological Collections and Biodiversity Data. He has participated on several projects on this topic, namely the Digitization of the Herbarium of the University of Coimbra, Digitization of the Botany Library and Archive, creation of several digital platforms such as the eHALOPH platform - halophytes database. In 2018, he completed his Master's in Ecology with the dissertation "Accelerating Digitization of Biological Collections for Fast Ecological Information Retrieval", which included the creation of EXPLORATOR, a crowdsourcing platform for the digitisation of biological collections. He has participated in Portuguese and International initiatives regarding Biodiversity Data and Digitisation.
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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

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
2018/11/27 - Current Science and Technology Management Centro de Ecologia Funcional, 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
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. 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
  2. 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. Sabine von Mering; Siobhan Leachman; Joaquim Santos; Heidi Meudt. "Engaging with Wikidata: Benefits and impacts for botanists and institutions". 2024.
    10.5281/zenodo.11102530
  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. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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. 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.

Other

Dataset
  1. Joaquim Santos; Santos, Joaquim. Natural history specimens collected and/or identified and deposited..
    10.5281/zenodo.8030869
  2. Ruben H. Heleno; José Costa; Filipe Covelo; Joaquim Santos; Sérgio Timóteo. Fruiting phenology data for 4,462 spontaneous and cultivated plant taxa in Portugal (1926 – 2013). 2024.
    10.6084/m9.figshare.25016432.v1
  3. 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
  4. Ruben H. Heleno; José Costa; Filipe Covelo; Joaquim Santos; Pedro Lopes; António Gouveia; Arménio Matos; et al. Support data for "O armário: Fruiting phenology data for 4,462 spontaneous and cultivated plant taxa in Portugal (1926 – 2013)". 2024.
    10.6084/m9.figshare.25016432
  5. 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
  6. Ruben H. Heleno; José Costa; Filipe Covelo; Joaquim Santos; Pedro Lopes; António Gouveia; Arménio Matos; et al. O armário: Fruiting phenology data for 4,462 spontaneous and cultivated plant taxa in Portugal (1926 – 2013). 2024.
    10.6084/m9.figshare.25016432.v5
Other output
  1. Online workshop Upskilling in Wikidata for maximum impact IBC 2024. 2024. Siobhan Leachman; Heidi Meudt; Sabine von Mering; Joaquim Santos.
    10.5281/zenodo.12741075
  2. 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