add bibtex references

docs/api/synvar/index.md

@@ -6,17 +6,17 @@
 
 ## Parameters
 
-* **ref**: Gene name or chromosome number or name (e.g. JAK2, BRAF, 9, X). Optional if an identifier is given in the variant parameter.
+* **ref**: Gene name or chromosome number or name (e.g. `JAK2`, `BRAF`, `9`, `X`). Optional if an identifier is given in the variant parameter.
 
-* **variant**: Variant description, COSMIC id, or dbSNP id (e.g. V617F, Val600Glu, rs113488022, COSM476). 
+* **variant**: Variant description, COSMIC id, or dbSNP id (e.g. `V617F`, `Val600Glu`, `rs113488022`, `COSM476`). 
 
-* **level**: Level of the provided variant description (protein, transcript, genome, dbsnp or cosmic).
+* **level**: Level of the provided variant description (`protein`, `transcript`, `genome`, `dbsnp` or `cosmic`).
 
 ## Optional parameters
 
-* **iso**: Validate on and generate synonyms for isoforms: false (default) or true.
-* **map**: Output syntactic variations even if the variant could not be mapped on genome: false (default) or true.
-* **format**: Output format: xml (default) or beacon (json).
+* **iso**: Validate on and generate synonyms for isoforms: `false` (default) or `true`.
+* **map**: Output syntactic variations even if the variant could not be mapped on genome: `false` (default) or `true`.
+* **format**: Output format: `xml` (default) or `beacon` (json).
 
 ## Examples
 

docs/biodiversitypmc/index.md

@@ -40,10 +40,11 @@ it allows to ask questions in natural languages, and to obtain answers extracted
 
 ## Reference
 
-SIBiLS are detailed in the 2020 web server issue of Nucleic Acids Research: [SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts](https://academic.oup.com/nar/article/48/W1/W12/5831752). Here is the graphical abstract designed for the publication :
-
+SIBiLS are detailed in the 2020 web server issue of Nucleic Acids Research: *SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts* [@10_1093_nar_gkaa328]. Here is the graphical abstract designed for the publication :
 
 <figure markdown>
   ![graphical abstract](../assets/graphical_abstract.png){ loading=lazy style="width: calc(min(100%, 35rem)); margin: auto;" }
   <figcaption></figcaption>
 </figure>
+
+See also *From sibils to biodiversity pmc: foundations for the one health library.* [@pasche2023sibils]

docs/synvar/index.md

@@ -12,7 +12,7 @@ hide:
 
 ## Background
 
-Genetic variants are drawing increasing interest regarding their role in pathologies, for designing new drugs or refining treatment efficacy through stratification. However, variant interpretation depends on time-consuming curation tasks. To support variant interpretation efforts and decisions based on the latest evidences, we propose [Variomes](../variomes/index.md) [1], a service performing variant-specific triage of publications. 
+Genetic variants are drawing increasing interest regarding their role in pathologies, for designing new drugs or refining treatment efficacy through stratification. However, variant interpretation depends on time-consuming curation tasks. To support variant interpretation efforts and decisions based on the latest evidences, we propose [Variomes](../variomes/index.md) [@pasche2021variomes], a service performing variant-specific triage of publications.
 
 To increase the comprehensiveness of Variomes, we developed SynVar. This tool enables the generation of synonyms and normalization of variants. This task faces different challenges: 
 
@@ -38,15 +38,15 @@ To enable a smooth and effective retrieval of variants in the literature, we dev
 
 ### Use-cases
 
-**Protein variant**: the change is validated on the reference sequence of the canonical isoform, by default, as retrieved by the NextProt API tool [2]. The valid variant is then backtranslated into the possible transcript variants, using the back-translator tool from Mutalyzer [3]. Finally the transcript variant is mapped onto its genomic position (GRCh37 and GRCh38 builds) using VariantValidator [4].
+* **Protein variant**: the change is   validated on the reference sequence of the canonical isoform, by default, as retrieved by the [NextProt API tool](https://api.nextprot.org/) [@zahn2020nextprot]. The valid variant is then backtranslated into the possible transcript variants, using the back-translator tool from [Mutalyzer](https://mutalyzer.nl/) [@den2016sequence]. Finally the transcript variant is mapped onto its genomic position (GRCh37 and GRCh38 builds) using [VariantValidator](https://rest.variantvalidator.org/) [@freeman2018variantvalidator].
 
-**Transcript variant**: the variant is validated and mapped onto genome position using VariantValidator. It is translated into protein variant using Mutalyzer.
+* **Transcript variant**: the variant is validated and mapped onto genome position using VariantValidator. It is translated into protein variant using Mutalyzer.
 
-**Genomic variant**: the variant is validated and converted to the transcript variants using VariantValidator, if not intergenic. Transcript variants are translated into protein variants using Mutalyzer. If intergenic, only genomic variant synonyms are generated.
+* **Genomic variant**: the variant is validated and converted to the transcript variants using VariantValidator, if not intergenic. Transcript variants are translated into protein variants using Mutalyzer. If intergenic, only genomic variant synonyms are generated.
 
-**dbSNP id**: The different genomic variants associated to the dbSNP [5] id are retrieved through the NCBI eutils services. The conversion and translation procedure from genomic variant is similar to the one described above.
+* **dbSNP id**: The different genomic variants associated to the dbSNP [@smigielski2000dbsnp] id are retrieved through the NCBI eutils services. The conversion and translation procedure from genomic variant is similar to the one described above.
 
-**COSMIC id**: The transcript variant corresponding to the COSMIC id is retrieved through the downloadable COSMIC data [6]. The genomic mapping and translation of transcript variant is similar to the one described above.
+* **COSMIC id**: The transcript variant corresponding to the COSMIC id is retrieved through the downloadable COSMIC data [@tate2019cosmic]. The genomic mapping and translation of transcript variant is similar to the one described above.
 
 ### Output
 
@@ -69,12 +69,3 @@ Results are returned as a list of genomic variants (unique position and change),
 ## API
 
 See [the dedicated page](../api/synvar/index.md)
-
-## References
-
-1. Pasche, E., Mottaz, A., Caucheteur, D., Gobeill, J., Michel, P.A., Ruch. P. (2021). Variomes: a high recall search engine to support the curation of genomic variants. bioRxiv : the preprint server for biology, 2021.05.29.446224. <https://doi.org/10.1101/2021.05.29.446224>
-1. Zahn-Zabal, M., Michel, P. A., Gateau, A., Nikitin, F., Schaeffer, M., Audot, E., Gaudet, P., Duek, P. D., Teixeira, D., Rech de Laval, V., Samarasinghe, K., Bairoch, A., & Lane, L. (2020). The neXtProt knowledgebase in 2020: data, tools and usability improvements. Nucleic acids research, 48(D1), D328–D334. <https://doi.org/10.1093/nar/gkz995>
-1. den Dunnen J. T. (2016). Sequence Variant Descriptions: HGVS Nomenclature and Mutalyzer. Current protocols in human genetics, 90, 7.13.1–7.13.19. <https://doi.org/10.1002/cphg.2>
-1. Freeman, P. J., Hart, R. K., Gretton, L. J., Brookes, A. J., & Dalgleish, R. (2018). VariantValidator: Accurate validation, mapping, and formatting of sequence variation descriptions. Human mutation, 39(1), 61–68. <https://doi.org/10.1002/humu.23348>
-1. Smigielski, E. M., Sirotkin, K., Ward, M., & Sherry, S. T. (2000). dbSNP: a database of single nucleotide polymorphisms. Nucleic acids research, 28(1), 352–355. <https://doi.org/10.1093/nar/28.1.352>
-1. Tate, J. G., Bamford, S., Jubb, H. C., Sondka, Z., Beare, D. M., Bindal, N., Boutselakis, H., Cole, C. G., Creatore, C., Dawson, E., Fish, P., Harsha, B., Hathaway, C., Jupe, S. C., Kok, C. Y., Noble, K., Ponting, L., Ramshaw, C. C., Rye, C. E., Speedy, H. E., … Forbes, S. A. (2019). COSMIC: the Catalogue Of Somatic Mutations In Cancer. Nucleic acids research, 47(D1), D941–D947. <https://doi.org/10.1093/nar/gky1015>

docs/variomes/index.md

@@ -17,7 +17,7 @@ hide:
 
 ## Introduction
 
-Precision oncology relies on the use of treatments targeting specific genetic variants. However, identifying clinically actionable variants as well as relevant information likely to be used to treat a patient with a given cancer is a labor-intensive task, which includes searching the literature for a large set of variants. The lack of universally adopted standard nomenclature for variants requires the development of variant-specific literature search engines. We develop a system to perform triage of publications relevant to support an evidence-based decision. Together with providing a ranked list of articles for a given variant, the system is also able to prioritize variants, as found in a Variant Calling Format, assuming that the clinical actionability of a genetic variant is correlated with the volume of literature published about the variant. Our system searches within four pre-annotated document collections: MEDLINE abstracts, PubMed Central full-text articles, supplementary materials associated with publications, and ClinicalTrials.gov clinical trials. A variant synonym generator is used to increase the comprehensiveness of the set of retrieved documents. We then apply different strategies to rank the publications.
+Precision oncology relies on the use of treatments targeting specific genetic variants. However, identifying clinically actionable variants as well as relevant information likely to be used to treat a patient with a given cancer is a labor-intensive task, which includes searching the literature for a large set of variants. The lack of universally adopted standard nomenclature for variants requires the development of variant-specific literature search engines. We develop a system to perform triage of publications relevant to support an evidence-based decision. Together with providing a ranked list of articles for a given variant, the system is also able to prioritize variants, as found in a Variant Calling Format, assuming that the clinical actionability of a genetic variant is correlated with the volume of literature published about the variant. Our system [@pasche2021variomes] searches within four pre-annotated document collections: MEDLINE abstracts, PubMed Central full-text articles, supplementary materials associated with publications, and ClinicalTrials.gov clinical trials. A variant synonym generator is used to increase the comprehensiveness of the set of retrieved documents. We then apply different strategies to rank the publications.
 
 ## API
 

mkdocs.yml

@@ -9,6 +9,7 @@ markdown_extensions:
   - tables
   - footnotes
   - def_list
+  - footnotes
   - pymdownx.tasklist:
       custom_checkbox: true
   - pymdownx.tabbed:
@@ -38,7 +39,9 @@ extra_css:
   - assets/extra.css
 
 plugins:
-   - swagger-ui-tag
+  - swagger-ui-tag
+  - bibtex:
+      bib_file: "refs.bib"
 
 #### nav section ####
 nav:

refs.bib

@@ -0,0 +1,87 @@
+@article{10_1093_nar_gkaa328,
+    author = {Gobeill, Julien and Caucheteur, Déborah and Michel, Pierre-André and Mottin, Luc and Pasche, Emilie and Ruch, Patrick},
+    title = "{SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts}",
+    journal = {Nucleic Acids Research},
+    volume = {48},
+    number = {W1},
+    pages = {W12-W16},
+    year = {2020},
+    month = {05},
+    abstract = "{Thanks to recent efforts by the text mining community, biocurators have now access to plenty of good tools and Web interfaces for identifying and visualizing biomedical entities in literature. Yet, many of these systems start with a PubMed query, which is limited by strong Boolean constraints. Some semantic search engines exploit entities for Information Retrieval, and/or deliver relevance-based ranked results. Yet, they are not designed for supporting a specific curation workflow, and allow very limited control on the search process. The Swiss Institute of Bioinformatics Literature Services (SIBiLS) provide personalized Information Retrieval in the biological literature. Indeed, SIBiLS allow fully customizable search in semantically enriched contents, based on keywords and/or mapped biomedical entities from a growing set of standardized and legacy vocabularies. The services have been used and favourably evaluated to assist the curation of genes and gene products, by delivering customized literature triage engines to different curation teams. SIBiLS (https://candy.hesge.ch/SIBiLS) are freely accessible via REST APIs and are ready to empower any curation workflow, built on modern technologies scalable with big data: MongoDB and Elasticsearch. They cover MEDLINE and PubMed Central Open Access enriched by nearly 2 billion of mapped biomedical entities, and are daily updated.}",
+    issn = {0305-1048},
+    doi = {10.1093/nar/gkaa328},
+    url = {https://academic.oup.com/nar/article/48/W1/W12/5831752},
+}
+@article{pasche2023sibils,
+  title={From SIBiLS to Biodiversity PMC: Foundations for the One Health Library},
+  author={Pasche, Emilie and Gobeill, Julien and Agosti, Donat and Penev, Lyubomir and Groom, Quentin and Georgiev, Teodor and Gaillac, Esteban and Flament, Alexandre and Caucheteur, D{\'e}borah and Michel, Pierre-Andr{\'e} and others},
+  journal={Biodiversity Information Science and Standards},
+  volume={7},
+  pages={e111660},
+  year={2023},
+  publisher={Pensoft Publishers},
+  doi={10.3897/biss.7.111660},
+}
+@article{pasche2021variomes,
+  title={Variomes: a high recall search engine to support the curation of genomic variants},
+  author={Pasche, Emilie and Mottaz, Ana{\"\i}s and Caucheteur, D{\'e}borah and Gobeill, Julien and Michel, Pierre-Andr{\'e} and Ruch, Patrick},
+  journal={bioRxiv: the preprint server for biology},
+  year={2021},
+  publisher={Cold Spring Harbor Laboratory},
+  doi={10.1101/2021.05.29.446224},
+}
+@article{zahn2020nextprot,
+  title={The neXtProt knowledgebase in 2020: data, tools and usability improvements},
+  author={Zahn-Zabal, Monique and Michel, Pierre-Andr{\'e} and Gateau, Alain and Nikitin, Fr{\'e}d{\'e}ric and Schaeffer, Mathieu and Audot, Estelle and Gaudet, Pascale and Duek, Paula D and Teixeira, Daniel and Rech de Laval, Valentine and others},
+  journal={Nucleic Acids Research},
+  volume={48},
+  number={D1},
+  pages={D328--D334},
+  year={2020},
+  publisher={Oxford University Press},
+  doi={10.1093/nar/gkz995},
+}
+@article{den2016sequence,
+  title={Sequence variant descriptions: HGVS nomenclature and mutalyzer},
+  author={den Dunnen, Johan T},
+  journal={Current Protocols in Human Genetics},
+  volume={90},
+  number={1},
+  pages={7--13},
+  year={2016},
+  publisher={Wiley Online Library},
+  doi={10.1002/cphg.2},
+}
+@article{freeman2018variantvalidator,
+  title={VariantValidator: Accurate validation, mapping, and formatting of sequence variation descriptions},
+  author={Freeman, Peter J and Hart, Reece K and Gretton, Liam J and Brookes, Anthony J and Dalgleish, Raymond},
+  journal={Human mutation},
+  volume={39},
+  number={1},
+  pages={61--68},
+  year={2018},
+  publisher={Wiley Online Library},
+  doi={10.1002/humu.23348},
+}
+@article{smigielski2000dbsnp,
+  title={dbSNP: a database of single nucleotide polymorphisms},
+  author={Smigielski, Elizabeth M and Sirotkin, Karl and Ward, Minghong and Sherry, Stephen T},
+  journal={Nucleic acids research},
+  volume={28},
+  number={1},
+  pages={352--355},
+  year={2000},
+  publisher={Oxford University Press},
+  doi={https://doi.org/10.1093/nar/28.1.352},
+}
+@article{tate2019cosmic,
+  title={COSMIC: the catalogue of somatic mutations in cancer},
+  author={Tate, John G and Bamford, Sally and Jubb, Harry C and Sondka, Zbyslaw and Beare, David M and Bindal, Nidhi and Boutselakis, Harry and Cole, Charlotte G and Creatore, Celestino and Dawson, Elisabeth and others},
+  journal={Nucleic acids research},
+  volume={47},
+  number={D1},
+  pages={D941--D947},
+  year={2019},
+  publisher={Oxford University Press},
+  doi={10.1093/nar/gky1015},
+}

requirements.txt

@@ -1,2 +1,3 @@
 mkdocs-material>=8.5.8
 mkdocs-swagger-ui-tag==0.6.10
+mkdocs-bibtex