From 8b52ba454ddcd17c0c8577d04cdbaf37c76da699 Mon Sep 17 00:00:00 2001 From: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> Date: Tue, 19 Dec 2023 15:13:17 +0100 Subject: [PATCH] Adding a bibliography (#1434) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Adding bibliography * Update style_guide.md (#1435) --------- Co-authored-by: Korbinian Bösl --- Gemfile | 1 + _bibliography/references.bib | 148 +++++++++++++++++++ _config.yml | 4 + pages/contribute/style_guide.md | 7 +- pages/your_domain/microbial_biotechnology.md | 52 ++----- 5 files changed, 171 insertions(+), 41 deletions(-) create mode 100644 _bibliography/references.bib diff --git a/Gemfile b/Gemfile index dd2b1788d..4c8effdfc 100644 --- a/Gemfile +++ b/Gemfile @@ -13,6 +13,7 @@ group :jekyll_plugins do gem 'jekyll-github-metadata', '~> 2.15' gem 'jekyll-relative-links', '~> 0.6' gem 'jekyll-seo-tag', '~> 2.8' + gem 'jekyll-scholar', '~> 7.1.3' gem 'jekyll-remote-theme' end diff --git a/_bibliography/references.bib b/_bibliography/references.bib new file mode 100644 index 000000000..90ef3f01a --- /dev/null +++ b/_bibliography/references.bib @@ -0,0 +1,148 @@ +@article{field2008migs, + title={The minimum information about a genome sequence (MIGS) specification}, + author={Field, D. and et al.}, + journal={Nature biotechnology}, + volume={26}, + number={5}, + pages={541--547}, + year={2008}, + doi={10.1038/nbt1360}, + url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2409278/} +} + +@article{ham2012jbeiice, + title={Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools}, + author={Ham, T. S. and et al.}, + journal={Nucleic acids research}, + volume={40}, + number={18}, + pages={e141}, + year={2012}, + doi={10.1093/nar/gks531}, + url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3467034/} +} + +@article{hecht2018bacterial, + title={A minimum information standard for reproducing bench-scale bacterial cell growth and productivity}, + author={Hecht, A. and et al.}, + journal={Communications biology}, + volume={1}, + pages={219}, + year={2018}, + doi={10.1038/s42003-018-0220-6}, + url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6283831/} +} + +@article{kuwahara2017sbolme, + title={SBOLme: a Repository of SBOL Parts for Metabolic Engineering}, + author={Kuwahara, H. and et al.}, + journal={ACS synthetic biology}, + volume={6}, + number={4}, + pages={732--736}, + year={2017}, + doi={10.1021/acssynbio.6b00278}, + url={https://pubmed.ncbi.nlm.nih.gov/28076956/} +} + +@article{maloy2007strain, + title={Strain Collections and Genetic Nomenclature}, + author={Maloy, S. R. and Hughes, K. T.}, + journal={Methods in Enzymology}, + pages={3--8}, + year={2007}, + doi={10.1016/s0076-6879(06)21001-2}, + url={https://pubmed.ncbi.nlm.nih.gov/17352909/} +} + +@article{parte2020lpsn, + title={List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ}, + author={Parte, A. C. and et al.}, + journal={International journal of systematic and evolutionary microbiology}, + volume={70}, + number={11}, + pages={5607--5612}, + year={2020}, + doi={10.1099/ijsem.0.004332}, + url={https://pubmed.ncbi.nlm.nih.gov/32701423/} +} + +@article{sainzdemurieta2016toward, + title={Toward the First Data Acquisition Standard in Synthetic Biology}, + author={Sainz de Murieta, I. and Bultelle, M. and Kitney, R. I.}, + journal={ACS synthetic biology}, + volume={5}, + number={8}, + pages={817--826}, + year={2016}, + doi={10.1021/acssynbio.5b00222}, + url={https://pubmed.ncbi.nlm.nih.gov/26854090/} +} + +@article{sarkans2018biostudies, + title={The BioStudies database—one stop shop for all data supporting a life sciences study}, + author={Sarkans, U. and et al.}, + journal={Nucleic Acids Research}, + pages={D1266--D1270}, + year={2018}, + doi={10.1093/nar/gkx965}, + url={https://pubmed.ncbi.nlm.nih.gov/29069414/} +} + +@article{spidlen2021data, + title={Data File Standard for Flow Cytometry, Version FCS 3.2}, + author={Spidlen, J. and et al.}, + journal={Cytometry. Part A: the journal of the International Society for Analytical Cytology}, + volume={99}, + number={1}, + pages={100--102}, + year={2021}, + doi={10.1002/cyto.a.24225}, + url={https://pubmed.ncbi.nlm.nih.gov/32881398/} +} + +@article{strenda2014standards, + title={Standards for Reporting Enzyme Data: The STRENDA Consortium: What it aims to do and why it should be helpful}, + journal={Perspectives in Science}, + volume={1}, + number={1-6}, + pages={131--137}, + year={2014}, + doi={10.1016/j.pisc.2014.02.012}, + url={https://www.sciencedirect.com/science/article/pii/S2213020914000135} +} + +@article{tellechealuzardo2020linking, + title={Linking Engineered Cells to Their Digital Twins: A Version Control System for Strain Engineering}, + author={Tellechea-Luzardo, J. and et al.}, + journal={ACS synthetic biology}, + volume={9}, + number={3}, + pages={536--545}, + year={2020}, + doi={10.1021/acssynbio.9b00400}, + url={https://pubmed.ncbi.nlm.nih.gov/32078768/} +} + +@article{tenhoopen2015m2b3, + title={Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards}, + author={Ten Hoopen, P. and et al.}, + journal={Standards in genomic sciences}, + volume={10}, + pages={20}, + year={2015}, + doi={10.1186/s40793-015-0001-5}, + url={https://pubmed.ncbi.nlm.nih.gov/26203332/} +} + +@article{zhang2017sboldesigner, + title={SBOLDesigner 2: An Intuitive Tool for Structural Genetic Design}, + author={Zhang, M. and et al.}, + journal={ACS synthetic biology}, + volume={6}, + number={7}, + pages={1150--1160}, + year={2017}, + doi={10.1021/acssynbio.6b00275}, + url={https://pubmed.ncbi.nlm.nih.gov/28441476/} +} diff --git a/_config.yml b/_config.yml index 5f9e29800..2e3a03eb1 100644 --- a/_config.yml +++ b/_config.yml @@ -135,6 +135,9 @@ defaults: values: sidebar: about +scholar: + style: modern-language-association + plugins: - elixir-toolkit-theme-plugins - jemoji @@ -142,3 +145,4 @@ plugins: - jekyll-sitemap - jekyll-github-metadata - jekyll-octicons + - jekyll-scholar diff --git a/pages/contribute/style_guide.md b/pages/contribute/style_guide.md index a496614e1..ca791d579 100644 --- a/pages/contribute/style_guide.md +++ b/pages/contribute/style_guide.md @@ -42,9 +42,10 @@ In general, we follow the European Commission's [Web Writing Style Guide](https: * This is item 3 of the list. * **Numbers:** spell the numbers one to ten out. After that, write the numbers (11, 12, 13, etc.). * **Quotations:** use double quotes for quotations, and single quotes for quotes within quotes. - * **References:** use the [Nature Author instructions](https://www.nature.com/srep/author-instructions/submission-guidelines#references) for books and papers. Use "*et al.*" for more than five authors. - * Bellin, D. L. *et al.* Electrochemical camera chip for simultaneous imaging of multiple metabolites in biofilms. Nat. Commun. 7, 10535; [10.1038/ncomms10535](http://www.nature.com/articles/ncomms10535) (2016). - * Lam, J. Data Management. (John Wiley & Sons, Inc., 2019). + * **References:** + * add your citations as bibtex to the `_bibliography/references.bib` file + * add `{% cite reference_key %}` to the text where you are citing the reference + * add `## Bibliography` `{% bibliography --cited %}` to show a bibliography section with cited refrences on a page. * **That/which:** use "that" when you are defining something and "which" when you are adding extra information about it e.g.: * "The cat that was on the table suddenly got up" is telling us which cat it was. It is important to the meaning of the sentence because you are not talking about any cat, just the cat on the table. * "The cat, which was sitting on the table, suddenly got up" is giving us extra information about the cat. The information is not necessary to understand the sentence. You can remove the clause and the sentence will still be clear. Clauses starting with "which" usually begin with a comma. diff --git a/pages/your_domain/microbial_biotechnology.md b/pages/your_domain/microbial_biotechnology.md index f62391e16..c7f3489f8 100644 --- a/pages/your_domain/microbial_biotechnology.md +++ b/pages/your_domain/microbial_biotechnology.md @@ -71,15 +71,15 @@ It is recommended to publish and share information about biological hosts in ded #### Metadata schemas and ontologies * Current data standards to capture the taxonomic and phenotypic data are still evolving, with notable work on the {% tool "access-to-biological-collection-data-schema" %} and the activities of the {% tool "biodiversity-information-standards" %}. The Darwin Core standard from the {% tool "biodiversity-information-standards" %} is an appropriate standard to provide metadata about the taxonomic properties of a particular microorganism. * The {% tool "ncbi-taxonomy" %}homepage can also provide appropriate taxon IDs for recording taxonomic information. -* Information about proposed standardised nomenclature for prokaryotes can be found at the {% tool "list-of-prokaryotic-names-with-standing-in-nomenclature" %} ([Parte et al., 2020](https://pubmed.ncbi.nlm.nih.gov/32701423/)). -* Data standards for recording the information about where a microorganism was isolated from do exist and this topic is covered in other RDMkit pages such as the [marine metagenomics](marine_metagenomics) domain. Information can also be found in a publication by Ten Hoopen and colleagues ([Ten Hoopen et al., 2015](https://pubmed.ncbi.nlm.nih.gov/26203332/)). +* Information about proposed standardised nomenclature for prokaryotes can be found at the {% tool "list-of-prokaryotic-names-with-standing-in-nomenclature" %} {% cite parte2020lpsn %}. +* Data standards for recording the information about where a microorganism was isolated from do exist and this topic is covered in other RDMkit pages such as the [marine metagenomics](marine_metagenomics) domain. Information can also be found in a publication by Ten Hoopen and colleagues {% cite tenhoopen2015m2b3 %}. * {% tool "the-environment-ontology" %} is also relevant here to describe environmental entities of all kinds, from microscopic to intergalactic scales. -* A set of genetic nomenclature standards have been established by microbiologists and have been used for many years. These are still a useful way of communicating data about the genotype of a strain ([Maloy and Hughes, 2007](https://pubmed.ncbi.nlm.nih.gov/17352909/)). -* Minimal information standards have been established to specify this metadata, such as the MIGS standard ([Field et al., 2008](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2409278/)). +* A set of genetic nomenclature standards have been established by microbiologists and have been used for many years. These are still a useful way of communicating data about the genotype of a strain {% cite maloy2007strain %}. +* Minimal information standards have been established to specify this metadata, such as the MIGS standard {% cite field2008migs %}. #### (Meta)data publication and sharing * For sharing host information, you can use databases such as the {% tool "bacdive" %}. You can also deposit strains and associated information in a strain repository such as the {% tool "ncimb" %} or the {% tool "atcc" %}. There are also many organisations established for individual species of microorganisms, the {% tool "bacillus-genetic-stock-center" %} being one example. -* Databases such as {% tool "cellrepo" %} allow strains that have been barcoded to be tracked using a version control type system ([Tellechea-Luzardo et al., 2020](https://pubmed.ncbi.nlm.nih.gov/32078768/)). +* Databases such as {% tool "cellrepo" %} allow strains that have been barcoded to be tracked using a version control type system {% cite tellechealuzardo2020linking %}. * Genomic information can be captured at the nucleotide level using the well-known {% tool "european-nucleotide-archive" %} and submitted to the ENA database to allow the information to be shared. * The database collection from the {% tool "international-nucleotide-sequence-database-collaboration" %} provides an umbrella for gathering and sharing a variety of sequence data from different sequence databases internationally. * Other databases such as {% tool "genbank" %} and the {% tool "dna-data-bank-of-japan" %} also cater for sequence information. @@ -101,7 +101,7 @@ Appropriate and detailed description of the synthetic parts design is critical f #### Existing data * Sequences are characterised as parts which can be found with the assistance of various repositories such as: * {% tool "igem-parts-registry" %} - * {% tool "jbei-ice" %} ([Ham et al., 2012](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3467034/)) + * {% tool "jbei-ice" %} {% cite ham2012jbeiice %} * {% tool "synbiohub" %} * {% tool "freegenes" %} - Repository of IP-free synthetic biological parts * Sequences can be isolated from standard genetic databases such as {% tool "european-nucleotide-archive" %} and {% tool "genbank" %}. @@ -109,9 +109,9 @@ Appropriate and detailed description of the synthetic parts design is critical f #### Tools for metadata collection * You can manage the design stage using genetic computer aided design tools, such as {% tool "benchling" %} for example, where information can be shared within small teams. {% tool "benchling" %} supports a number of different data standards including FASTA, GenBank and SBOL1. * Sometimes FASTA will be the most relevant format, for example when sending for DNA synthesis. - * Formats like GenBank, DICOM-SB ([Sainz de Murieta, Bultelle and Kitney, 2016](https://pubmed.ncbi.nlm.nih.gov/26854090/)) or SBOL may be more applicable for instances where more information, such as functional annotation, would be useful to be shared. + * Formats like GenBank, DICOM-SB {% cite sainzdemurieta2016toward %} or SBOL may be more applicable for instances where more information, such as functional annotation, would be useful to be shared. * SBOL 2.0 and higher allows more than just the genetics of a system to be captured and shared. Using SBOL allows interactions between components in the design to be specified, information about RNA and proteins can be included and the provenance of a design can also be captured. Experimental information relating to the test and build of a system can also be captured and shared. -* SBOL data can be made using tools such as {% tool "benchling" %} (SBOL1 only), {% tool "sboldesigner" %} ([Zhang et al., 2017](https://pubmed.ncbi.nlm.nih.gov/28441476/)) and {% tool "shortbol" %} to name but a few. A more comprehensive list of SBOL tools can be found on the {% tool "synthetic-biology-open-language" %} website. +* SBOL data can be made using tools such as {% tool "benchling" %} (SBOL1 only), {% tool "sboldesigner" %} {% cite zhang2017sboldesigner %} and {% tool "shortbol" %} to name but a few. A more comprehensive list of SBOL tools can be found on the {% tool "synthetic-biology-open-language" %} website. * More generally, the [Investigation/Study/Assay (ISA)](https://isa-specs.readthedocs.io/) model can be used in systems biology, life sciences, environmental and biomedical domains to structure research outputs. The [ISA-Tab](https://isa-specs.readthedocs.io/en/latest/isatab.html) format provides a framework for capturing these data in CSV files. * {% tool "rightfield" %} provides a mechanism for capturing metadata using easy to use spreadsheets. @@ -142,7 +142,7 @@ Here we describe some of the available options to accurately represent and store * More generally, the {% tool "iupac-iubmb-joint-commission-on-biochemical-nomenclature" %} encourages the communication of biochemical information using generally understood terminology. #### (Meta)data publication -* Databases such as SBOLME ([Kuwahara et al., 2017](https://pubmed.ncbi.nlm.nih.gov/28076956/)) or {% tool "synbiohub" %} can be used to share the data. +* Databases such as SBOLME {% cite kuwahara2017sbolme %} or {% tool "synbiohub" %} can be used to share the data. * Metabolite information can also be submitted to, or referred to in, {% tool "chebi" %}. * {% tool "brenda" %} (BRENDA). @@ -210,13 +210,13 @@ The data arising from assays for product development is highly variable and beyo ### Solutions #### Metadata standards -* **Minimum Information Standard for Engineered Organism Experiments (MIEO).** Minimal information necessary to record the growth of an organism in culture, has been described by Hect and colleagues ([Hecht et al., 2018](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6283831/)). +* **Minimum Information Standard for Engineered Organism Experiments (MIEO).** Minimal information necessary to record the growth of an organism in culture, has been described by Hect and colleagues {% cite hecht2018bacterial %}. -* **Enzyme.** If your product is a protein such as an enzyme then some standards developed by the {% tool "standards-for-reporting-enzyme-data" %} may be helpful ([‘Standards for Reporting Enzyme Data: The STRENDA Consortium: What it aims to do and why it should be helpful’, 2014](https://www.sciencedirect.com/science/article/pii/S2213020914000135)). +* **Enzyme.** If your product is a protein such as an enzyme then some standards developed by the {% tool "standards-for-reporting-enzyme-data" %} may be helpful {% cite strenda2014standards %}. * **Microscopy.** Microscopy is often also used to characterise the behaviour of engineered microorganisms. Standards such as the [Open Microscopy Environment Ontology](https://fairsharing.org/bsg-s001430/) and the {% tool "cellular-microscopy-phenotype-ontology" %} can help provide standardised metadata terms. -* **Flow Cytometry data.** The {% tool "international-society-for-the-advancement-of-cytometry" %} provides information on a variety of appropriate data standards for capturing Flow Cytometry data (used to characterise microbial populations at a single cell level) ([Spidlen et al., 2021](https://pubmed.ncbi.nlm.nih.gov/32881398/)). +* **Flow Cytometry data.** The {% tool "international-society-for-the-advancement-of-cytometry" %} provides information on a variety of appropriate data standards for capturing Flow Cytometry data (used to characterise microbial populations at a single cell level) {% cite spidlen2021data %}. * **Nucleic acids information.** The {% tool "european-nucleotide-archive" %}, amongst others, provides guidance on the metadata for RNAseq datasets. @@ -234,33 +234,9 @@ The data arising from assays for product development is highly variable and beyo * {% tool "arrayexpress" %} * **Proteomics.** Proteomics data can be shared via {% tool "proteomics-standards-initiative" %}. * **Metabolic studies.** Metabolomic studies can be shared through the {% tool "metabolomexchange" %}, which provides a resource for sharing data from metabolic studies and guidance for the submission of metabolome data. -* **Biological sources.** Information about biological sources can be shared via the {% tool "biostudies" %} database, which has been set up to capture and share information about multi-omics and other biological studies ([Sarkans et al., 2018](https://pubmed.ncbi.nlm.nih.gov/29069414/)). +* **Biological sources.** Information about biological sources can be shared via the {% tool "biostudies" %} database, which has been set up to capture and share information about multi-omics and other biological studies {% cite sarkans2018biostudies %}. ## Bibliography -[Field, D. et al. (2008) ‘The minimum information about a genome sequence (MIGS) specification’, Nature biotechnology, 26(5), pp. 541–547. doi: 10.1038/nbt1360.](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2409278/) - -[Ham, T. S. et al. (2012) ‘Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools’, Nucleic acids research, 40(18), p. e141. doi: 10.1093/nar/gks531.](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3467034/) - -[Hecht, A. et al. (2018) ‘A minimum information standard for reproducing bench-scale bacterial cell growth and productivity’, Communications biology, 1, p. 219. doi: 10.1038/s42003-018-0220-6.](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6283831/) - -[Kuwahara, H. et al. (2017) ‘SBOLme: a Repository of SBOL Parts for Metabolic Engineering’, ACS synthetic biology, 6(4), pp. 732–736. doi: 10.1021/acssynbio.6b00278.](https://pubmed.ncbi.nlm.nih.gov/28076956/) - -[Maloy, S. R. and Hughes, K. T. (2007) ‘Strain Collections and Genetic Nomenclature’, Methods in Enzymology, pp. 3–8. doi: 10.1016/s0076-6879(06)21001-2.](https://pubmed.ncbi.nlm.nih.gov/17352909/) - -[Parte, A. C. et al. (2020) ‘List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ’, International journal of systematic and evolutionary microbiology, 70(11), pp. 5607–5612. doi: 10.1099/ijsem.0.004332.](https://pubmed.ncbi.nlm.nih.gov/32701423/) - -[Sainz de Murieta, I., Bultelle, M. and Kitney, R. I. (2016) ‘Toward the First Data Acquisition Standard in Synthetic Biology’, ACS synthetic biology, 5(8), pp. 817–826. doi: 10.1021/acssynbio.5b00222.](https://pubmed.ncbi.nlm.nih.gov/26854090/) - -[Sarkans, U. et al. (2018) ‘The BioStudies database—one stop shop for all data supporting a life sciences study’, Nucleic Acids Research, pp. D1266–D1270. doi: 10.1093/nar/gkx965.](https://pubmed.ncbi.nlm.nih.gov/29069414/) - -[Spidlen, J. et al. (2021) ‘Data File Standard for Flow Cytometry, Version FCS 3.2’, Cytometry. Part A: the journal of the International Society for Analytical Cytology, 99(1), pp. 100–102. doi: 10.1002/cyto.a.24225.](https://pubmed.ncbi.nlm.nih.gov/32881398/) - -[‘Standards for Reporting Enzyme Data: The STRENDA Consortium: What it aims to do and why it should be helpful’ (2014) Perspectives in Science, 1(1-6), pp. 131–137. doi: 10.1016/j.pisc.2014.02.012.](https://www.sciencedirect.com/science/article/pii/S2213020914000135) - -[Tellechea-Luzardo, J. et al. (2020) ‘Linking Engineered Cells to Their Digital Twins: A Version Control System for Strain Engineering’, ACS synthetic biology, 9(3), pp. 536–545. doi: 10.1021/acssynbio.9b00400.](https://pubmed.ncbi.nlm.nih.gov/32078768/) - -[Ten Hoopen, P. et al. (2015) ‘Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards’, Standards in genomic sciences, 10, p. 20. doi: 10.1186/s40793-015-0001-5.](https://pubmed.ncbi.nlm.nih.gov/26203332/) - -[Zhang, M. et al. (2017) ‘SBOLDesigner 2: An Intuitive Tool for Structural Genetic Design’, ACS synthetic biology, 6(7), pp. 1150–1160. doi: 10.1021/acssynbio.6b00275.](https://pubmed.ncbi.nlm.nih.gov/28441476/) +{% bibliography --cited %}