From 69dab63a2cfabc81f8824005cae6e7c6c57d575a Mon Sep 17 00:00:00 2001
From: Sandra Derozier <sandra.derozier@inrae.fr>
Date: Thu, 6 Apr 2023 22:04:23 +0200
Subject: [PATCH 1/3] \#10 - Update - April 2023
---
templates/release.html | 102 ++++++++++++++++++++++++++++++++++++-----
1 file changed, 90 insertions(+), 12 deletions(-)
diff --git a/templates/release.html b/templates/release.html
index 7921100..e1472a5 100644
--- a/templates/release.html
+++ b/templates/release.html
@@ -31,7 +31,96 @@
<div class="card" style="border-color: #21517A;">
<div class="card-header text-center" style="background-color: #21517A; border-color: #21517A; color: #fff;">
- Omnicrobe 1.1 (<i>current release</i>)
+ Omnicrobe 1.2 (<i>current release</i>)
+ </div>
+ <div class="card-body">
+ <p align='justify'>
+ <h5 class="text-info">Information about the data</h5>
+ <ul>
+ <li>Ontologies used: <a href="http://agroportal.lirmm.fr/ontologies/ONTOBIOTOPE" target="_blank">OntoBiotope</a> version 2022-04-28 & <a href="https://forgemia.inra.fr/omnicrobe/extended-microorganisms-taxonomy" target="_blank">Taxonomy</a> version 2023-02-24.</li>
+ </ul>
+ <div style="margin-left: 15%;margin-right: 15%;">
+ <table class="table table-sm table-striped">
+ <caption class="text-center">Versions and number of relationships per source</caption>
+ <thead>
+ <tr>
+ <th scope="col"></th>
+ <th class="text-right" scope="col">PubMed</th>
+ <th class="text-right" scope="col">GenBank</th>
+ <th class="text-right" scope="col">DSMZ</th>
+ <th class="text-right" scope="col">CIRM-BIA</th>
+ <th class="text-right" scope="col">CIRM-CFBP</th>
+ <th class="text-right" scope="col">CIRM-Levures</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <th scope="row">Version</th>
+ <td class="text-right">2023-03-27</td>
+ <td class="text-right">2023-03-27</td>
+ <td class="text-right">2023-03-27</td>
+ <td class="text-right">2023-02-09</td>
+ <td class="text-right">2023-03-16</td>
+ <td class="text-right">2021-10-14</td>
+ </tr>
+ <tr>
+ <th scope="row">Taxa - Habitat relations</th>
+ <td class="text-right">764,796</td>
+ <td class="text-right">268,781</td>
+ <td class="text-right">51,176</td>
+ <td class="text-right">682</td>
+ <td class="text-right">1,223</td>
+ <td class="text-right">942</td>
+ </tr>
+ <tr>
+ <th scope="row">Taxa - Phenotype relations</th>
+ <td class="text-right">53,377</td>
+ <td class="text-right">-</td>
+ <td class="text-right">-</td>
+ <td class="text-right">-</td>
+ <td class="text-right">-</td>
+ <td class="text-right">-</td>
+ </tr>
+ <tr>
+ <th scope="row">Taxa - Use relations</th>
+ <td class="text-right">18,145</td>
+ <td class="text-right">-</td>
+ <td class="text-right">-</td>
+ <td class="text-right">-</td>
+ <td class="text-right">-</td>
+ <td class="text-right">-</td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+
+ <h5 class="text-info">New features and improvements in this release</h5>
+ <ul>
+ <li>improved extraction quality</li>
+ <li>fixed bugs</li>
+ <li>updated taxonomy</li>
+ </ul>
+ <!-- <h5 class="text-info">Fixed in this release</h5>
+ <ul>
+ <li>...</li>
+ </ul> -->
+ <!--h5 class="text-info">Source code</h5>
+ <ul>
+ <li>Text-mining workflow: GitHub repository (<a class="text-info" target="_blank" href="https://creativecommons.org/licenses/by/2.0/deed.en">CC-BY license</a>).</li>
+ <li>Web interface: GitHub repository (<a class="text-info" target="_blank" href="https://creativecommons.org/licenses/by/2.0/deed.en">CC-BY license</a>).</li>
+ </ul-->
+ </p>
+ </div>
+ <div class="card-footer text-center" style="background-color: #21517A; border-color: #21517A; color: #fff;">
+ 6 April 2023
+ </div>
+ </div>
+ <br/>
+ <p><h4 class="text-info">Previous releases</h4></p>
+
+ <div class="card" style="border-color: #21517A;">
+ <div class="card-header text-center" style="background-color: #21517A; border-color: #21517A; color: #fff;">
+ Omnicrobe 1.1
</div>
<div class="card-body">
<p align='justify'>
@@ -100,15 +189,6 @@
<li>fixed bugs</li>
<li>updated taxonomy</li>
</ul>
- <!-- <h5 class="text-info">Fixed in this release</h5>
- <ul>
- <li>...</li>
- </ul> -->
- <!--h5 class="text-info">Source code</h5>
- <ul>
- <li>Text-mining workflow: GitHub repository (<a class="text-info" target="_blank" href="https://creativecommons.org/licenses/by/2.0/deed.en">CC-BY license</a>).</li>
- <li>Web interface: GitHub repository (<a class="text-info" target="_blank" href="https://creativecommons.org/licenses/by/2.0/deed.en">CC-BY license</a>).</li>
- </ul-->
</p>
</div>
<div class="card-footer text-center" style="background-color: #21517A; border-color: #21517A; color: #fff;">
@@ -116,8 +196,6 @@
</div>
</div>
<br/>
- <p><h4 class="text-info">Previous releases</h4></p>
-
<div class="card" style="border-color: #21517A;">
<div class="card-header text-center" style="background-color: #21517A; border-color: #21517A; color: #fff;">
Omnicrobe 1.0
--
GitLab
From b2e6919e7f9d4f80d3e3682d28f5de547c678f39 Mon Sep 17 00:00:00 2001
From: Sandra Derozier <sandra.derozier@inrae.fr>
Date: Thu, 6 Apr 2023 22:13:48 +0200
Subject: [PATCH 2/3] \#10 - Update - April 2023
---
templates/release.html | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/templates/release.html b/templates/release.html
index e1472a5..47b66fd 100644
--- a/templates/release.html
+++ b/templates/release.html
@@ -61,7 +61,7 @@
<td class="text-right">2023-03-27</td>
<td class="text-right">2023-02-09</td>
<td class="text-right">2023-03-16</td>
- <td class="text-right">2021-10-14</td>
+ <td class="text-right">2022-10-14</td>
</tr>
<tr>
<th scope="row">Taxa - Habitat relations</th>
@@ -150,7 +150,7 @@
<td class="text-right">2022-10-26</td>
<td class="text-right">2022-09-30</td>
<td class="text-right">2022-10-07</td>
- <td class="text-right">2021-10-14</td>
+ <td class="text-right">2022-10-14</td>
</tr>
<tr>
<th scope="row">Taxa - Habitat relations</th>
--
GitLab
From 26bb6ba745e23e099bad2e7ed8b64f48844d58ec Mon Sep 17 00:00:00 2001
From: Sandra Derozier <sandra.derozier@inrae.fr>
Date: Thu, 6 Apr 2023 22:53:21 +0200
Subject: [PATCH 3/3] Bibliography
---
templates/about.html | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/templates/about.html b/templates/about.html
index e85b2d5..773ab71 100644
--- a/templates/about.html
+++ b/templates/about.html
@@ -103,7 +103,9 @@
<br/><p align="justify"><b><span style="color: #21517A;">Omnicrobe database</span></b><br/>
<p> <b><span style="color: #516eb0;">Posters</span></b><br/>
- <ul><li><div align="justify">Dérozier, S., Deléger, L., Chaix, E., Mekdad R., Ba, M., Bossy, R., Sicard, D., Loux, V., Falentin, H. & Nédellec, C. <a target="_blank" href="https://hal.inrae.fr/hal-02904156">Florilege: a database gathering microbial habitats, phenotypes and uses</a>. Presented at <i>JOBIM 2020</i>, virtual edition (2020-06-30 - 2020-07-03).</div></li>
+ <ul><li><div align="justify">Dérozier, S., Bossy, R., Deléger, L., Ba, M., Chaix, E., Loux, V., Falentin, H., Nédellec, C. <a target="_blank" href="https://hal.inrae.fr/hal-04061565v1">Omnicrobe, an open-access database of microbial habitats, phenotypes and uses extracted from text</a>. Presented at <i>JOBIM 2022</i>, Rennes (2022-07-05 - 2022-07-08).</div></li>
+ <li><div align="justify">Falentin, H., Harlé, O., Dérozier, S., Deléger, L., Chaix, E., Ba, M., Bossy, R., Loux, V., Nédellec, C. <a target="_blank" href="https://hal.inrae.fr/hal-03694214v1">Omnicrobe : une base de données d’habitats et de phénotypes microbiens</a>. Presented at <i>23ème édition du colloque du Club des Bactéries Lactiques</i>, Rennes (2022-06-08 - 2022-06-10).</div></li>
+ <li><div align="justify">Dérozier, S., Deléger, L., Chaix, E., Mekdad R., Ba, M., Bossy, R., Sicard, D., Loux, V., Falentin, H. & Nédellec, C. <a target="_blank" href="https://hal.inrae.fr/hal-02904156">Florilege: a database gathering microbial habitats, phenotypes and uses</a>. Presented at <i>JOBIM 2020</i>, virtual edition (2020-06-30 - 2020-07-03).</div></li>
<li><div align="justify">Chaix, E., Dérozier, S., Deléger, L., Falentin, H., Bohuon, J.B., Ba, M., Bossy, R., Sicard, D., Loux, V. & Nédellec, C. <a target="_blank" href="https://hal.inrae.fr/hal-01827946v1">Florilege: an integrative database using text mining and ontologies</a>. In: <i>Abstract JOBIM 2018 (p. 563)</i>. Presented at JOBIM 2018, Marseille, FRA (2018-07-03 - 2018-07-06).</div></li>
<li><div align="justify">Falentin, H., Chaix, E., Dérozier, S., Weber, M., Buchin, S., Dridi, B., Deutsch, S.-M., Valence-Bertel, F., Casaregola, S., Renault, P., Champomier-Vergès, M.-C., Thierry, A., Zagorec, M., Irlinger, F., Delbès, C., Aubin, S., Bessières, P., Loux, V., Bossy, R., Dibie, J., Sicard, D., Nédellec, C. (2017, October). <a target="_blank" href="https://hal-montpellier-supagro.archives-ouvertes.fr/hal-01651302/">Florilege: a database gathering microbial phenotypes of food interest</a>. In <i>4th International Conference on Microbial Diversity 2017</i>, Bari, ITA (2017-10-24 - 2017-10-26).</div></li></ul></p>
--
GitLab