Add BMC Bioinformatics article

Author: pmonnin

README.md

@@ -4,6 +4,10 @@ A lightweight and simple ontology to reconcile and trace knowledge in pharmacoge
 
 PGxO is also available on the [NCBO BioPortal](https://bioportal.bioontology.org/ontologies/PGXO).
 
+A full description of the motivation, implementation and instantiation of PGxO is available in [2].
+
+When citing PGxO, please use [2].
+
 ## Documentation
 
 Documentation is available in the ``doc/`` folder:
@@ -32,7 +36,34 @@ PGxO: A very lite ontology to reconcile pharmacogenomic knowledge units.
 In _Methods, tools & platforms for Personalized Medicine in the Big Data Era_.
 [Link](https://hal.inria.fr/hal-01593184/document)
 2. Monnin, P., Legrand, J., Husson, G., Ringot, P., Tchechmedjiev, A.,
-Jonquet, C., Napoli, A., & Coulet, A. (2018). PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison. bioRxiv, 390971. [Link](https://doi.org/10.1101/390971)
+Jonquet, C., Napoli, A., & Coulet, A.
+PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, 
+enabling further comparison. BMC Bioinformatics 20-S(4): 139:1-139:16 (2019). 
+[Link](https://doi.org/10.1186/s12859-019-2693-9)
+
+```
+@Article{Monnin2019,
+    author="Monnin, Pierre
+    and Legrand, Jo{\"e}l
+    and Husson, Graziella
+    and Ringot, Patrice
+    and Tchechmedjiev, Andon
+    and Jonquet, Cl{\'e}ment
+    and Napoli, Amedeo
+    and Coulet, Adrien",
+    title="PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison",
+    journal="BMC Bioinformatics",
+    year="2019",
+    month="Apr",
+    day="18",
+    volume="20-S",
+    number="4",
+    pages="139",
+    issn="1471-2105",
+    doi="10.1186/s12859-019-2693-9",
+    url="https://doi.org/10.1186/s12859-019-2693-9"
+}
+```
 
 ## Acknowledgments
 

doc/MIRO.md

@@ -47,7 +47,10 @@ PGxO: A very lite ontology to reconcile pharmacogenomic knowledge units.
 In _Methods, tools & platforms for Personalized Medicine in the Big Data Era_.
 [Link](https://hal.inria.fr/hal-01593184/document)
 2. Monnin, P., Legrand, J., Husson, G., Ringot, P., Tchechmedjiev, A.,
-Jonquet, C., Napoli, A., & Coulet, A. (2018). PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison. bioRxiv, 390971. [Link](https://doi.org/10.1101/390971)
+Jonquet, C., Napoli, A., & Coulet, A.
+PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, 
+enabling further comparison. BMC Bioinformatics 20-S(4): 139:1-139:16 (2019). 
+[Link](https://doi.org/10.1186/s12859-019-2693-9)
 3. Matentzoglu, N., Malone, J., Mungall, C., Stevens, R.: MIRO: guidelines for
 minimum information for the reporting of an ontology. J. Biomedical Semantics
 9(1), 6–1613 (2018). doi:10.1186/s13326-017-0172-7

doc/pgxo.html

@@ -24,6 +24,45 @@ <h2>Introduction</h2>
             This URL should be used to import the ontology in another service, such as Protégé.
         </p>
 
+        <p>
+            Documentation, examples and issue reporting can be found on 
+            <a href="https://github.com/practikpharma/PGxO">GitHub</a>.<br />
+            A full description of the motivation, implementation and instantiation of PGxO 
+            is available in the <a href="https://doi.org/10.1186/s12859-019-2693-9">related publication</a>.
+        </p>
+
+        <h2>Citing PGxO</h2>
+        <p>
+            When citing PGxO, please use the following reference:<br />
+            Monnin, P., Legrand, J., Husson, G., Ringot, P., Tchechmedjiev, A.,
+            Jonquet, C., Napoli, A., &amp; Coulet, A.
+            PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, 
+            enabling further comparison. BMC Bioinformatics 20-S(4): 139:1-139:16 (2019). 
+        </p>
+        <pre><code>
+@Article{Monnin2019,
+    author="Monnin, Pierre
+    and Legrand, Jo{\"e}l
+    and Husson, Graziella
+    and Ringot, Patrice
+    and Tchechmedjiev, Andon
+    and Jonquet, Cl{\'e}ment
+    and Napoli, Amedeo
+    and Coulet, Adrien",
+    title="PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison",
+    journal="BMC Bioinformatics",
+    year="2019",
+    month="Apr",
+    day="18",
+    volume="20-S",
+    number="4",
+    pages="139",
+    issn="1471-2105",
+    doi="10.1186/s12859-019-2693-9",
+    url="https://doi.org/10.1186/s12859-019-2693-9"
+}
+        </code></pre>
+
         <h2>Index</h2>
 
         <h3 id="causes">causes</h3>