Merge pull request #6 from pierrelarmande/main

trombinoscope/publication/pierre-larmande.bib

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+@article{droc_orygenesdb_2009,
+	title = {{OryGenesDB} 2008 update: database interoperability for functional genomics of rice},
+	volume = {37},
+	doi = {10.1093/nar/gkn821},
+	number = {Database},
+	journal = {Nucleic Acids Research},
+	author = {Droc, G. and Perin, C. and Fromentin, S. and Larmande, P.},
+	month = jan,
+	year = {2009},
+	pages = {D992--D995},
+}
+
+@article{larmande_oryza_2008,
+	title = {Oryza {Tag} {Line}, a phenotypic mutant database for the {Genoplante} rice insertion line library},
+	volume = {36},
+	doi = {10.1093/nar/gkm762},
+	number = {Database issue},
+	journal = {Nucleic Acids Res.},
+	author = {Larmande, Pierre and Gay, Céline and Lorieux, Mathias and Périn, Christophe and Bouniol, Matthieu and Droc, Gaëtan and Sallaud, Christophe and Perez, Pascual and Barnola, Isabelle and Biderre-Petit, Corinne and Martin, Jérôme and Morel, Jean Benoît and Johnson, Alexander A. T. and Bourgis, Fabienne and Ghesquière, Alain and Ruiz, Manuel and Courtois, Brigitte and Guiderdoni, Emmanuel},
+	month = jan,
+	year = {2008},
+	pages = {D1022--1027},
+}
+
+@article{droc_orygenesdb:_2006,
+	title = {{OryGenesDB}: a database for rice reverse genetics},
+	volume = {34},
+	doi = {10.1093/nar/gkj012},
+	number = {Database issue},
+	journal = {Nucleic Acids Res.},
+	author = {Droc, G. and Ruiz, M. and Larmande, P. and Pereira, A. and Piffanelli, P. and Morel, J. B. and Dievart, A. and Courtois, B. and Guiderdoni, E. and Périn, C.},
+	month = jan,
+	year = {2006},
+	pages = {D736--740},
+}
+
+@article{jonquet_agroportal:_2018,
+	title = {{AgroPortal}: {A} vocabulary and ontology repository for agronomy},
+	volume = {144},
+	doi = {10.1016/j.compag.2017.10.012},
+	journal = {Computers and Electronics in Agriculture},
+	author = {Jonquet, Clément and Toulet, Anne and Arnaud, Elizabeth and Aubin, Sophie and Dzalé Yeumo, Esther and Emonet, Vincent and Graybeal, John and Laporte, Marie-Angélique and Musen, Mark A. and Pesce, Valeria and Larmande, Pierre},
+	month = jan,
+	year = {2018},
+	pages = {126--143},
+}
+
+@article{sempere_gigwagenotype_2016,
+	title = {Gigwa—{Genotype} investigator for genome-wide analyses},
+	volume = {5},
+	doi = {10.1186/s13742-016-0131-8},
+	number = {1},
+	journal = {GigaScience},
+	author = {Sempéré, Guilhem and Philippe, Florian and Dereeper, Alexis and Ruiz, Manuel and Sarah, Gautier and Larmande, Pierre},
+	month = jun,
+	year = {2016},
+	pages = {25},
+}
+
+@article{abbeloos_brapi_2019,
+	title = {{BrAPI} - an {Application} {Programming} {Interface} for {Plant} {Breeding} {Applications}},
+	doi = {10.1093/bioinformatics/btz190},
+	author = {Abbeloos, Rafael and Vasques Costa, Bruno and Edwards, Jeremy D and Papoutsoglou, Evangelia and Finkers, Richard and Verouden, Maikel and Robbins, Kelly and Selby, Peter and Glaser, Philip and Sun, Qi and Gao, Star Yanxin and Laporte, Marie-Angélique and Rouard, Mathieu and Guignon, Valentin and Kilian, Andrzej and Pearce, Brian and Uszynski, Grzegorz and Hok, Puthick and Larmande, Pierre and LeBauer, David and Marshall, David and Stephen, Gordon and Milne, Iain and Shaw, Paul and Raubach, Sebastian and Mistry, Naymesh and Backlund, Jan Erik and Tovar, Clarysabel and Soldevilla, Nahuel and Neveu, Pascal and Ramirez-Gonzalez, Ricardo H and Rathore, Abhishek and Sarma, Chaitanya and Rife, Trevor and Simon, Reinhard and Basterrechea Salido, Martin and Lange, Matthias and Ghaffar, Mehmood and König, Patrick and Scholz, Uwe and Lyon, David and Bauchet, Guillaume and Morales, Nicolas and Mueller, Lukas and Perez-Masias, Ivan and Benites-Alfaro, Omar and Birkett, Clay and Matthews, Dave and Raque, Angel M and Lagare, Jack Elendil B and Calaminos, Viana C and Sempéré, Guilhem and Carceller, Pierre and Pommier, Cyril and Cornut, Guillaume},
+	month = mar,
+	year = {2019},
+}
+
+
+@article{grant_agbiodata_2018,
+	title = {{AgBioData} consortium recommendations for sustainable genomics and genetics databases for agriculture},
+	volume = {2018},
+	doi = {10.1093/database/bay088},
+	journal = {Database},
+	author = {Grant, David and Nelson, Rex and Cannon, Steve and Harper, Lisa and Andorf, Carson and Cannon, Ethalinda K S and Condon, Bradford and Staton, Margaret and Cooper, Laurel and Jaiswal, Pankaj and Naithani, Sushma and Unni, Deepak and Dunn, Nathan and Elsik, Christine G and Farmer, Andrew and Grau, Emily and Wegrzyn, Jill and Herndon, Nic and Park, Carissa and Reecy, James and Hu, Zhi-Liang and Jonquet, Clement and Larmande, Pierre and Lazo, Gerard and Sen, Taner Z and Campbell, Jacqueline and McCarthy, Fiona and Menda, Naama and Mungall, Christopher J and Munoz-Torres, Monica C and Nesdill, Daureen and Sanderson, Lacey-Anne and Wang, Liya and Tello-Ruiz, Marcela Karey and Williams, Jason and Woodhouse, Margaret and Main, Doreen and Yu, Jing and Humann, Jodi and Jung, Sook and Ficklin, Stephen P and Unda, Victor and Poelchau, Monica and Walls, Ramona and Arnaud, Elizabeth and Laporte, Marie-Angélique and Reiser, Leonore and Subramaniam, Sabarinath and Berardini, Tanya Z and Birkett, Clayton and Ware, Doreen and Carson, James},
+	month = sep,
+	year = {2018},
+	keywords = {cloud computing, market oriented computing, utility computing, virtualization, \#nosource},
+}
+
+
+@article{do_pyrice_2020,
+	title = {{PyRice}: a {Python} package for querying {Oryza} {Sativa} databases},
+	doi = {10.1093/bioinformatics/btaa694},
+	journal = {Bioinformatics},
+	author = {Do, Quan and Hai, Ho Bich and Larmande, Pierre},
+	year = {2020},
+}
+
+@article{guilhem_gigwa_2019,
+	title = {Gigwa v2 – {Extended} and improved genotype investigator},
+	volume = {8},
+	doi = {10.1093/gigascience/giz051},
+	number = {5},
+	journal = {GigaScience},
+	author = {Guilhem, Sempéré and Adrien, Pétel and Mathieu, Rouard and Julien, Frouin and Yann, Hueber and Fabien, De Bellis and Pierre, Larmande},
+	year = {2019},
+	pages = {giz051},
+}
+
+@article{juanillas_v_rice_2019,
+	title = {Rice {Galaxy}: an open resource for plant science},
+	volume = {8},
+	doi = {10.1101/358754},
+	number = {5},
+	journal = {Gigascience},
+	author = {{Juanillas V} and {Dereeper A} and {Beaume N} and {Droc G} and {Dizon J} and {Mendoza JR} and {Perdon JP} and {Mansueto L} and {Triplett L} and {Lang J} and {Zhou G} and {Ratharanjan K} and {Plale B} and {Haga J} and {Larmande P} and {Mauleon RP}},
+	month = may,
+	year = {2019},
+	pages = {giz028},
+}
+
+@article{wollbrett_clever_2013,
+	title = {Clever generation of rich {SPARQL} queries from annotated relational schema: application to {Semantic} {Web} {Service} creation for biological databases},
+	volume = {14},
+	doi = {10.1186/1471-2105-14-126},
+	number = {1},
+	journal = {BMC Bioinformatics},
+	author = {Wollbrett, Julien and Larmande, Pierre and Lamotte, Frédéric de and Ruiz, Manuel},
+	year = {2013},
+	pages = {126},
+}
+
+@article{larmande_oryzagp_2021,
+	title = {{OryzaGP} 2021 update: a rice gene and protein dataset for named-entity recognition},
+	volume = {19},
+	doi = {10.5808/gi.21015},
+	number = {3},
+	journal = {Genomics Inform},
+	author = {Larmande, Pierre and Liu, Yusha and Yao, Xinzhi and Xia, Jingbo},
+	month = sep,
+	year = {2021},
+	pages = {e27},
+}
+
+@article{venkatesan_agronomic_2018,
+	title = {Agronomic {Linked} {Data} ({AgroLD}): {A} knowledge-based system to enable integrative biology in agronomy},
+	volume = {13},
+	doi = {10.1371/journal.pone.0198270},
+	number = {11},
+	journal = {PLoS One},
+	author = {Venkatesan, Aravind and Tagny Ngompe, Gildas and Hassouni, Nordine El and Chentli, Imene and Guignon, Valentin and Jonquet, Clement and Ruiz, Manuel and Larmande, Pierre},
+	year = {2018},
+	pages = {e0198270},
+}

trombinoscope/staff/pierre-larmande.yaml

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+# Please fill in your details and delete comments.
+# Please consider trying to keep this file up to date.
+#
+# This template contains dummy data for a fictional person,
+# "Jhon Doe".
+#
+# The line saying "---" should be the first line of your file.
+# No line should be longer than 80 characters.
+# Your file should be called "<firstname>-<lastname>.yaml".
+---
+#
+# Your real name, the exact way that you want it displayed.
+#
+staffname: Pierre Larmande 
+#
+# Most people will have "type: staff", but some may be "affiliate".
+#
+type: staff
+#
+# Change to "true"
+#
+active: true
+#
+# Your email address.
+#
+email: [email protected]
+#
+phone: xxx-xxx xx xx
+#
+# Use "city:" to say what city your main official workplace is
+# located in.  This is a list for people that are genuinely working
+# in different places.
+#
+city:
+  - Montpellier
+#
+workplace: IRD Montpellier
+#
+affiliation: IRD
+#
+# The SouthGreen facility that you are part of. 
+#
+facility: SouthGreen
+#
+# Current categories (pick one):
+# annotation, development, genomics, management, metabolomics,
+# proteomics, software, statistics, structure, systems biology,
+# dataservices, administration
+#
+category: 
+  - development
+  - annotation 
+  - dataservices
+  - systems biology
+#
+# Page to link to from your profile page (rarely used).
+#
+homepage: https://sites.google.com/site/larmandepierre
+#
+# Use "bibtex:" only if you have a separate BibTeX file in the
+# "publications" subdirectory.
+#
+bibtex: pierre-larmande.bib
+#
+# If you have an ORCID ID ("NNNN-NNNN-NNNN-NNNN")
+#
+orcid: 0000-0002-2923-9790 
+#
+# The name of an image file in the "img" subdirectory, no more than
+# about 400 pixels wide and less than 200 KB in file size.
+#
+image: pierre-larmande.jpg
+#
+# A list of lowercase keywords relevant to you.
+#
+keywords:
+  - functional genomics
+  - data integration
+  - ontologies
+  - post-GWAS analysis
+  - knowledge graphs
+  - text mining
+  - AI
+#
+# "role:" is the role that you play within your infrastructure.
+#
+role: Researcher 
+#
+bio:
+   Pierre Larmande is senior researcher at IRD, the French Public Research Institute for Sustainable Development. He is member of the DIADE Unit in Montpellier. His main research interests are Data integration, Semantic Web, plant-ontologies, semantic data linking, Knowledge management and Big Data for plant genomics.
+
+
+ He obtained PhD in Informatics from the university of Montpellier in 2007 (about federated plant data integration approaches applied to agronomy) and recently obtained the habilitation to conduct research supervision (HDR) in 2020. He coordinated the Oryza Tag Line phenotypic rice mutant database and was involved in the OrygenesDB T-DNA rice database.
+
+
+ Pierre Larmande is the lead PI of the Agronomic Linked Data project (AgroLD), which is a Knowledge Graph database that consists of data integrated from a variety of plant resources and ontologies. 
+
+
+