From 279623e5be077433b359e3a4a19ae57e4a0967b5 Mon Sep 17 00:00:00 2001 From: anjali Date: Fri, 25 May 2018 15:44:06 +0100 Subject: [PATCH 01/10] updating poms for 4.2.13-SNAPSHOT development --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index c21160b54..cea294f59 100644 --- a/pom.xml +++ b/pom.xml @@ -18,7 +18,7 @@ uk.ac.ebi.intact.service.sandbox intact-view war - 4.2.12-SNAPSHOT + 4.2.13-SNAPSHOT IntAct Services :: View From 012a540ec9ef934777aab64ea74ecf16fd242115 Mon Sep 17 00:00:00 2001 From: anjali Date: Fri, 25 May 2018 15:45:00 +0100 Subject: [PATCH 02/10] updating develop poms to master versions to avoid merge conflicts --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index cea294f59..c49a7ec4b 100644 --- a/pom.xml +++ b/pom.xml @@ -18,7 +18,7 @@ uk.ac.ebi.intact.service.sandbox intact-view war - 4.2.13-SNAPSHOT + 4.2.12 IntAct Services :: View From 4286594bb29419834f519b1b7f3b6c9d07b61bda Mon Sep 17 00:00:00 2001 From: anjali Date: Fri, 25 May 2018 15:45:00 +0100 Subject: [PATCH 03/10] Updating develop poms back to pre merge state --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index c49a7ec4b..cea294f59 100644 --- a/pom.xml +++ b/pom.xml @@ -18,7 +18,7 @@ uk.ac.ebi.intact.service.sandbox intact-view war - 4.2.12 + 4.2.13-SNAPSHOT IntAct Services :: View From acfe7e328ef058034bbd2590dcab612568536d03 Mon Sep 17 00:00:00 2001 From: ntoro Date: Mon, 22 Oct 2018 14:18:41 +0100 Subject: [PATCH 04/10] INTACTVIEW-48: Correct RNAcentral example and spelling. --- src/main/webapp/pages/search/search_panel.xhtml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/main/webapp/pages/search/search_panel.xhtml b/src/main/webapp/pages/search/search_panel.xhtml index ccde7877c..cf9182c1a 100644 --- a/src/main/webapp/pages/search/search_panel.xhtml +++ b/src/main/webapp/pages/search/search_panel.xhtml @@ -67,10 +67,10 @@ target="#{userQuery.searchQuery}"/> -
  • RNACentral ID: - RNAcentral ID: + -
    • From 4fcdcf4d6f5b975e75276303f825aac748824932 Mon Sep 17 00:00:00 2001 From: ntoro Date: Fri, 17 Apr 2020 19:50:38 +0100 Subject: [PATCH 05/10] Update version of dataexchange to make it compile again. Some dependencies used in previous versions of dataexchange are not available anymore. --- pom.xml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pom.xml b/pom.xml index cea294f59..feb6bd76f 100644 --- a/pom.xml +++ b/pom.xml @@ -32,7 +32,7 @@ 2.6.5 - 2.1.10 + 3.0.42 3.1.2.RELEASE false @@ -511,7 +511,7 @@ uk.ac.ebi.intact.dataexchange intact-cvutils - 2.1.9 + ${dataexchange.version} lucene @@ -527,7 +527,7 @@ uk.ac.ebi.intact.dataexchange.psimi intact-psixml-exchange - 2.1.9 + ${dataexchange.version} cpdetector @@ -572,7 +572,7 @@ uk.ac.ebi.intact.dataexchange.psimi intact-solr-core - 2.1.9.3 + ${dataexchange.version} woodstox From b2b97376e7ed2d59fbbb9cc15c96d7782fb7a24b Mon Sep 17 00:00:00 2001 From: ntoro Date: Fri, 17 Apr 2020 19:51:56 +0100 Subject: [PATCH 06/10] Add new datasets like coronavirus and rare diseases. --- .../documentation/downloads_content.xhtml | 115 ++++++++++++-- .../webapp/pages/resources/datasets.xhtml | 142 ++++++++++++++++-- 2 files changed, 230 insertions(+), 27 deletions(-) diff --git a/src/main/webapp/pages/documentation/downloads_content.xhtml b/src/main/webapp/pages/documentation/downloads_content.xhtml index e814000fb..3afad0d50 100644 --- a/src/main/webapp/pages/documentation/downloads_content.xhtml +++ b/src/main/webapp/pages/documentation/downloads_content.xhtml @@ -121,19 +121,19 @@ style="border:0px solid"/> -
  • - - Cardiac - - - Interactions involving cardiac related proteins - - - -
    • +
  • + + Cardiac + + - Interactions involving cardiac related proteins + + + +
  • @@ -147,6 +147,30 @@ style="border:0px solid"/>
    • +
  • + + Coronavirus + + - Interactions investigated in the context of Coronavirus. + + + +
    • +
  • + + Crohn's disease + + - Interactions of proteins identified as having a link to Crohn's disease. + + + +
  • @@ -171,7 +195,42 @@ - +
    • +
  • + + Huntington's + + - Publications describing interactions involved in Huntington's disease. + + + +
    • +
  • + + IBD + + - Inflammatory bowel disease + + + +
    • +
  • + + Neurodegeneration + + - Publications depicting interactions involved in neurodegenerative diseases + + +
    • +
  • + + Rare diseases + + - Interactions investigated in the context of Rare genetic disease + + + +
    • +
  • + + Ulcerative colitis + + - Interactions of proteins identified as having a link to ulcerative colitis + + + +

    • Computationally maintained datasets

    @@ -233,13 +316,13 @@
  • + value="http://www.ebi.ac.uk/intact/query/annot:"dataset:pdbe""> PDBe - Data obtained from the Protein Data Bank Europe + value="ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psi25/datasets/PDBe.zip"> diff --git a/src/main/webapp/pages/resources/datasets.xhtml b/src/main/webapp/pages/resources/datasets.xhtml index 4df6b42c3..706b721e7 100644 --- a/src/main/webapp/pages/resources/datasets.xhtml +++ b/src/main/webapp/pages/resources/datasets.xhtml @@ -69,7 +69,7 @@ value="http://www.ebi.ac.uk/intact/query/annot:"dataset:alzheimers""> Alzheimers - - Interaction dataset based on proteins with an association to Alzheimer disease + - Interaction dataset based on proteins with an association to Alzheimer disease. BioCreative - - Critical Assessment of Information Extraction systems in Biology + - Critical Assessment of Information Extraction systems in Biology. Cancer - - Interactions investigated in the context of cancer + - Interactions investigated in the context of cancer. Cardiac - - Interactions involving cardiac related proteins + - Interactions involving cardiac related proteins. Chromatin - - Epigenetic interactions resulting in chromatin modulation + - Epigenetic interactions resulting in chromatin modulation.
    • +
  • + + Coronavirus + + - Interactions investigated in the context of Coronavirus. + + + + +

    + Dataset of molecular interactions extracted from publications involving viral proteins from + the Coronaviridae family and human proteins, along with a certain proportion of other model organisms. The + data features mostly protein-protein and some RNA-protein interactions and covers SARS-CoV2 and + SARS-CoV primarily, with some interactions from other members of Coronaviridae as well. + Interactions between human proteins relevant for SARS-CoV2 infection have also been included. +

    +
    • +
  • + + Crohn's disease + + - Interactions of proteins identified as having a link to Crohn's disease. + + + + +

    + Interactions extracted from publications focused on proteins involved in Crohn's disease. +

    +
  • Cyanobacteria - - Interaction dataset based on Cyanobacteria proteins and related species + - Interaction dataset based on Cyanobacteria proteins and related species. Diabetes - - Interactions investigated in the context of Diabetes + - Interactions investigated in the context of Diabetes.
    • +
  • + + Huntington's + + - Publications describing interactions involved in Huntington's disease. + + + +

    + Interactions extracted from publications focused on proteins involved in Huntington's disease. +

    +
    • +
  • + + IBD + + - Inflammatory bowel disease + + + +

    + Interactions extracted from publications focused on proteins involved in Inflammatory Bowel Disease. +

    +
    • +
  • + + Neurodegeneration + + - Publications depicting interactions involved in neurodegenerative diseases + + + +

    + Interactions extracted from publications focused on proteins involved in neurodegenerative diseases. +

    +
  • @@ -260,6 +341,43 @@ LEAPS Award 2012.

    • +
  • + + Rare diseases + + - Interactions investigated in the context of Rare genetic disease + + + + +

    + This is a dataset of molecular interactions extracted from publications focused on the study of + any rare disease. 'A rare disease' is defined according to the European Union Regulation on + Orphan Medicinal Products (1999): a disease that affects not more than 1 person per 2000 in + the European population. The dataset is enriched with experimentally proven impact of clinical + mutations on interactions, and also with the non-clinical mutations which are found to have + effect on protein functionality. +

    +
    • +
  • + + Ulcerative colitis + + - Interactions of proteins identified as having a link to ulcerative colitis + + + + +

    + Interactions extracted from publications focused on proteins involved in ulcerative colitis. +

    +

    • Computationally maintained datasets

    @@ -331,22 +449,24 @@
  • + value="http://www.ebi.ac.uk/intact/query/annot:"dataset:pdbe""> PDBe - Data obtained from the Protein Data Bank Europe + value="ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psi25/datasets/PDBe.zip">

    - The Protein Data Bank in Europe (PDB3) is the European project for the collection, management and distribution of data + The Protein Data Bank in Europe (PDBe) is the European project for the collection, management and distribution of data about macromolecular structures, in collaboration with Worldwide Protein Data Bank (wwPDB). + href="http://www.wwpdb.org/" target="_blank">wwPDB). IntAct has incorporated a subset of the data from this database involving heterodimeric protein interactions.

    • From 282bce29470e73a1dd11b37541e5df665a4181f2 Mon Sep 17 00:00:00 2001 From: ntoro Date: Fri, 17 Apr 2020 19:52:32 +0100 Subject: [PATCH 07/10] Try to solve CORS problem with Reactome. --- .../webapp/resources/javascript/reactome-analysis.js | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/main/webapp/resources/javascript/reactome-analysis.js b/src/main/webapp/resources/javascript/reactome-analysis.js index cf327bb6e..e259dfa57 100644 --- a/src/main/webapp/resources/javascript/reactome-analysis.js +++ b/src/main/webapp/resources/javascript/reactome-analysis.js @@ -3,13 +3,13 @@ var reactomeAnalysis = function(btn, query, negative, spoke, projection) { var reactomeCorsURI; if (projection) { - reactomeCorsURI = 'http://www.reactome.org/AnalysisService/identifiers/url/projection?pageSize=0&page=1'; + reactomeCorsURI = 'https://www.reactome.org/AnalysisService/identifiers/url/projection?pageSize=0&page=1'; } else { - reactomeCorsURI = 'http://www.reactome.org/AnalysisService/identifiers/url?pageSize=0&page=1'; + reactomeCorsURI = 'https://www.reactome.org/AnalysisService/identifiers/url?pageSize=0&page=1'; } // ToDo: make this URI configurable to support local testing. perhaps pass in as argument - var dataURI = "http://www.ebi.ac.uk/intact/list?query="+ query+"&negative="+negative+"&spoke="+spoke; + var dataURI = "https://www.ebi.ac.uk/intact/list?query="+ query+"&negative="+negative+"&spoke="+spoke; var parent = $('.reactomeResults'); parent.text("Loading..."); @@ -29,7 +29,7 @@ var reactomeAnalysis = function(btn, query, negative, spoke, projection) { parent.text(""); if (data.pathwaysFound > 0) {// results in Reactome btn3.get(0).onclick = function(){ - window.open("http://www.reactome.org/PathwayBrowser/#DTAB=AN&ANALYSIS=" + data.summary.token, "_blank"); + window.open("https://www.reactome.org/PathwayBrowser/#DTAB=AN&ANALYSIS=" + data.summary.token, "_blank"); }; btn3.removeClass("reactome-results-hidden").addClass("reactome-results"); parent.removeClass("reactome-loading").addClass("reactome-results"); @@ -58,7 +58,7 @@ var reactomeAnalysis = function(btn, query, negative, spoke, projection) { var reactomeAnalysisList = function() { - var reactomeCorsURI = 'http://www.reactome.org/AnalysisService/identifiers/?pageSize=0&page=1&sortBy=ENTITIES_PVALUE&order=ASC&resource=TOTAL'; + var reactomeCorsURI = 'https://www.reactome.org/AnalysisService/identifiers/?pageSize=0&page=1&sortBy=ENTITIES_PVALUE&order=ASC&resource=TOTAL'; var parent = $('.reactomeResults'); var btn = $('.viewReactome'); From b4400c9ecb3b66f9dbfe9af0f7c0c928677ab1e5 Mon Sep 17 00:00:00 2001 From: ntoro Date: Fri, 17 Apr 2020 19:54:02 +0100 Subject: [PATCH 08/10] Adds banner for COVID-19 to home page. --- src/main/webapp/home_content.xhtml | 26 +++++++++++++++++++++++--- src/main/webapp/images/psi30.png | Bin 0 -> 2321 bytes 2 files changed, 23 insertions(+), 3 deletions(-) create mode 100644 src/main/webapp/images/psi30.png diff --git a/src/main/webapp/home_content.xhtml b/src/main/webapp/home_content.xhtml index b396d7653..779644420 100644 --- a/src/main/webapp/home_content.xhtml +++ b/src/main/webapp/home_content.xhtml @@ -1,10 +1,30 @@ -
    -
    +
    +
    + COVID19-related interactions at IntAct's Coronavirus dataset.
    + More info: Dataset description
    + Browse: Coronavirus dataset
    + Download: FTP Coronavirus dataset in + + + + + + +
    +
    +
    +

    IntAct Molecular Interaction Database

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