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|
<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>
|
