diff --git a/pom.xml b/pom.xml index c49a7ec4b..a8a7e9d49 100644 --- a/pom.xml +++ b/pom.xml @@ -18,21 +18,21 @@ uk.ac.ebi.intact.service.sandbox intact-view war - 4.2.12 + 4.2.13 IntAct Services :: View - scm:git:https://github.com/EBI-IntAct/intact-view.git - scm:git:https://github.com/EBI-IntAct/intact-view.git - https://github.com/EBI-IntAct/intact-view + scm:git:https://github.com/EBI-IntAct/former-intact-view.git + scm:git:https://github.com/EBI-IntAct/former-intact-view.git + https://github.com/EBI-IntAct/former-intact-view HEAD 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 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

diff --git a/src/main/webapp/images/psi30.png b/src/main/webapp/images/psi30.png new file mode 100644 index 000000000..1ffa753df Binary files /dev/null and b/src/main/webapp/images/psi30.png differ 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.

    • 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: + -
    • 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');