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Diffstat (limited to 'gn2/wqflask/templates/show_trait_details.html')
| -rw-r--r-- | gn2/wqflask/templates/show_trait_details.html | 255 |
1 files changed, 255 insertions, 0 deletions
diff --git a/gn2/wqflask/templates/show_trait_details.html b/gn2/wqflask/templates/show_trait_details.html new file mode 100644 index 00000000..9c12393d --- /dev/null +++ b/gn2/wqflask/templates/show_trait_details.html @@ -0,0 +1,255 @@ +<table class="table"> + <tr> + <td><b>Group</b></td> + <td>{{ this_trait.dataset.group.species[0]|upper }}{{ this_trait.dataset.group.species[1:] }}: {{ this_trait.dataset.group.name }} group</td> + </tr> + {% if this_trait.dataset.type == 'Publish' %} + <tr> + <td><b>Phenotype</b></td> + <td><div>{{ this_trait.description_fmt }}</div></td> + </tr> + <tr> + <td><b>Authors</b></td> + <td><div>{{ this_trait.authors }}</div></td> + </tr> + <tr> + <td><b>Title</b></td> + <td><div>{{ this_trait.title }}</div></td> + </tr> + <tr> + <td><b>Journal</b></td> + <td>{{ this_trait.journal }} ({% if this_trait.pubmed_id %}<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ this_trait.pubmed_id }}&dop=Abstract" target="_blank" title="PubMed">{{ this_trait.year }}</a>{% else %}{{ this_trait.year }}{% endif %})</td> + </tr> + {% elif this_trait.dataset.type == 'ProbeSet' %} + <tr> + <td><b>Tissue</b></td> + <td>{{ this_trait.dataset.tissue }}</td> + </tr> + {% endif %} + {% if this_trait.dataset.type == 'ProbeSet' %} + {% if this_trait.symbol != None %} + <tr> + <td><b>Gene Symbol</b></td> + <td>{{ this_trait.symbol }}</td> + </tr> + {% endif %} + <tr> + <td><b>Aliases</b></td> + <td>Wikidata: {{ this_trait.wikidata_alias_fmt|replace(",",";") }}</td> + </tr> + {% if this_trait.alias_fmt != "Not Available" %} + <tr> + <td></td> + <td>GeneNetwork: {{ this_trait.alias_fmt|replace(",",";") }}</td> + </tr> + {% endif %} + {% endif %} + {% if this_trait.dataset.type != 'Publish' %} + <tr> + <td><b>Location</b></td> + <td>{{ this_trait.location_fmt }}</td> + </tr> + {% endif %} + {% if ncbi_summary != None and ncbi_summary != "" %} + <tr> + <td><b>Summary</b></td> + <td>{{ ncbi_summary }}</td> + </tr> + {% endif %} + <tr> + <td><b>Database</b></td> + <td> + <a href="http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName={{ dataset.name }}" target="_blank"> + {{ dataset.fullname }} + </a> + <br/> + <a href="{{ url_for('get_dataset', name=dataset.name) }}" target="_blank"> + GN2 Link: {{ dataset.fullname }} + </a> + </td> + </tr> + {% if this_trait.probe_set_specificity %} + <tr> + <td><b>Target Score</b></td> + <td> + <a href="http://gn1.genenetwork.org/blatInfo.html" target="_blank" title="Values higher than 2 for the specificity are good"> + BLAT Specificity + </a>: + {{ "%0.3f" | format(this_trait.probe_set_specificity|float) }} + + {% if this_trait.probe_set_blat_score %} + Score: {{ "%0.3f" | format(this_trait.probe_set_blat_score|float) }} + {% endif %} + </td> + </tr> + {% endif %} + {% if this_trait.pubmed_id or this_trait.geneid or this_trait.omim or this_trait.symbol %} + <tr> + <td><b>Resource Links</b></td> + <td> + {% if pubmed_link %} + <a href="{{ pubmed_link }}" target="_blank" title="PubMed"> + PubMed + </a> + {% endif %} + {% if ncbi_gene_link %} + <a href="{{ ncbi_gene_link }}" target="_blank" title="Info from NCBI Entrez Gene"> + Gene + </a> + + {% endif %} + {% if omim_link %} + <a href="{{ omim_link }}" target="_blank" title="Summary from On Mendelion Inheritance in Man"> + OMIM + </a> + + {% endif %} + {% if genemania_link %} + <a href="{{ genemania_link }}" target="_blank" title="GeneMANIA"> + GeneMANIA + </a> + + {% endif %} + {% if protein_atlas_link %} + <a href="{{ protein_atlas_link }}" target="_blank" title="Human Protein Atlas"> + Protein Atlas + </a> + + {% endif %} + {% if open_targets_link %} + <a href="{{ open_targets_link }}" target="_blank" title="Open Targets"> + Open Targets + </a> + + {% endif %} + {% if homologene_link %} + <a href="{{ homologene_link }}" target="_blank" title="Find similar genes in other species"> + HomoloGene + </a> + + {% endif %} + {% if this_trait.symbol %} + <!-- + <a href="{{ genotation_link }}" target="_blank" title="Related descriptive, genomic, clinical, functional and drug-therapy information"> + Genotation + </a> + + --> + {% if rgd_link %} + <a href="{{ rgd_link }}" target="_blank"> + Rat Genome DB + </a> + + {% endif %} + <a href="{{ gtex_link }}" target="_blank" title="GTEx Portal"> + GTEx Portal + </a> + + {% if phenogen_link %} + <a href="{{ phenogen_link }}" target="_blank"> + PhenoGen + </a> + + {% endif %} + {% if genebridge_link %} + <a href="{{ genebridge_link }}" target="_blank"> + GeneBridge + </a> + {% endif %} + {% endif %} + <br> + {% if ucsc_blat_link %} + <a href="{{ ucsc_blat_link }}" target="_blank" title="Info from UCSC Genome Browser"> + UCSC + </a> + + {% endif %} + {% if biogps_link %} + <a href="{{ biogps_link }}" target="_blank" title="Expression across many tissues and cell types"> + BioGPS + </a> + + {% endif %} + {% if string_link %} + <a href="{{ string_link }}" target="_blank" title="Protein interactions: known and inferred"> + STRING + </a> + + {% endif %} + {% if panther_link %} + <a href="{{ panther_link }}" target="_blank" title="Gene and protein data resources from Celera-ABI"> + PANTHER + </a> + + {% endif %} + {% if gemma_link %} + <a href="{{ gemma_link }}" target="_blank" title="Meta-analysis of gene expression data"> + Gemma + </a> + + {% endif %} + {% if aba_link %} + <a href="{{ aba_link }}" target="_blank" title="Allen Brain Atlas"> + ABA + </a> + + {% endif %} + {% if ebi_gwas_link %} + <a href="{{ ebi_gwas_link }}" target="_blank" title="EBI GWAS"> + EBI GWAS + </a> + + {% endif %} + {% if wiki_pi_link %} + <a href="{{ wiki_pi_link }}" target="_blank" title="Wiki-Pi"> + Wiki-Pi + </a> + + {% endif %} + {% if uniprot_link %} + <a href="{{ uniprot_link }}" target="_blank" title="UniProt"> + UniProt + </a> + + {% endif %} + </td> + </tr> + {% endif %} +</table> + +<div class="btn-toolbar"> + <div class="btn-group"> + <button type="button" id="add_to_collection" class="btn btn-success" title="Add to Collection">Add</button> + {% if this_trait.dataset.type == 'ProbeSet' or this_trait.dataset.type == 'Geno' %} + {% if this_trait.symbol != None %} + <button type="button" class="btn btn-default" title="Find similar expression data" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&gene={{ this_trait.symbol }}&alias=1&species={{ dataset.group.species }}', '_blank')">Find</button> + {% endif %} + {% if UCSC_BLAT_URL != "" %} + <button type="button" class="btn btn-default" title="Check probe locations at UCSC" onclick="window.open('{{ UCSC_BLAT_URL }}', '_blank')">Verify</button> + {% endif %} + {% if this_trait.symbol != None %} + <button type="button" class="btn btn-default" title="Write or review comments about this gene" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol={{ this_trait.symbol }}', '_blank')">(GN1) GeneWiki</button> + {% if dataset.group.species == "mouse" or dataset.group.species == "rat" %} + <button type="button" class="btn btn-default" title="View SNPs and Indels" onclick="window.open('/snp_browser?first_run=true&species={{ dataset.group.species }}&gene_name={{ this_trait.symbol }}&limit_strains=on', '_blank')">SNPs</button> + {% endif %} + {% endif %} + {% if show_probes == "True" %} + <button type="button" class="btn btn-default" title="Check sequence of probes" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?FormID=showProbeInfo&database={{ this_trait.dataset.name }}&ProbeSetID={{ this_trait.name }}&CellID={{ this_trait.cellid }}&RISet={{ dataset.group.name }}&incparentsf1=ON', '_blank')">Probes</button> + {% endif %} + {% endif %} + <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}', '_blank')">Go to GN1</button> + {% if this_trait.dataset.type == 'Publish' %} + <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/datasets/{{ this_trait.dataset.group.id }}/traits/{{ this_trait.name }}?resource-id={{ resource_id }}&dataset_name={{this_trait.dataset.name}}', '_blank')">Edit</button> + {% endif %} + + {% if this_trait.dataset.type == 'ProbeSet' %} + <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/datasets/traits/{{ this_trait.name }}?resource-id={{ resource_id }}&dataset_name={{this_trait.dataset.name}}', '_blank')">Edit</button> + {% endif %} + </div> + {%if "group:resource:edit-resource" in trait_privileges%} + <div class="btn-group"> + <button type="button" id="edit_resource" class="btn btn-success" title="Edit Privileges" onclick="window.open('{{url_for('oauth2.resource.view_resource', resource_id=resource_id)}}', '_blank')">Edit Privileges</button> + </div> + {% endif %} +</div> + |