From 46d2d532f773994d63163e31ba75ad4fd471d083 Mon Sep 17 00:00:00 2001 From: stuartmiyasato Date: Thu, 13 Jun 2024 13:28:52 -0700 Subject: [PATCH 1/4] Update robots.txt --- src/encoded/static/robots.txt | 57 ++++++++++++++++++++++++----------- 1 file changed, 40 insertions(+), 17 deletions(-) diff --git a/src/encoded/static/robots.txt b/src/encoded/static/robots.txt index 7acad9a9cdb..8b89c0fcfe8 100644 --- a/src/encoded/static/robots.txt +++ b/src/encoded/static/robots.txt @@ -36,6 +36,22 @@ Disallow: /encode-software Disallow: /region-search Disallow: /brain-matrix Disallow: /encyclopedia/* +Disallow: /deeply-profiled-uniform-batch-matrix +Disallow: /deeply-profiled-uniform-batch-matrix/ +Disallow: /deeply-profiled-matrix +Disallow: /deeply-profiled-matrix/ +Disallow: /degron-matrix +Disallow: /degron-matrix/ +Disallow: /encore-matrix +Disallow: /encore-matrix/ +Disallow: /stem-cell-matrix +Disallow: /stem-cell-matrix/ +Disallow: /immune-cells +Disallow: /immune-cells/ +Disallow: /mouse-development-matrix +Disallow: /mouse-development-matrix/ +Disallow: /functional-characterization-matrix +Disallow: /functional-characterization-matrix/ Allow: /encode-software/?type=Software Allow: /region-search/ Allow: /rnaget/ @@ -79,23 +95,30 @@ Allow: /entex-matrix/?type=Experiment&status=released&internal_tags=ENTEx$ Allow: /reference-epigenome-matrix/?type=Experiment&related_series.@type=ReferenceEpigenome&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens$ Allow: /reference-epigenome-matrix/?type=Experiment&related_series.@type=ReferenceEpigenome&replicates.library.biosample.donor.organism.scientific_name=Mus+musculus$ Allow: /matrix/?type=Experiment&status=released&internal_tags=ENCORE$ -Allow: /sescc-stem-cell-matrix/?type=Experiment&internal_tags=SESCC$ Allow: /mouse-development-matrix/?type=Experiment&status=released&related_series.@type=OrganismDevelopmentSeries&replicates.library.biosample.organism.scientific_name=Mus+musculus$ -Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Homo%20sapiens&assay_title=Histone%20ChIP-seq&status=released$ -Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Homo%20sapiens&assay_title=Histone%20ChIP-seq&status=released$ -Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Homo%20sapiens&assay_title=Histone%20ChIP-seq&status=released$ -Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Homo%20sapiens&assay_title=Histone%20ChIP-seq&status=released$ -Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Homo%20sapiens&assay_title=TF%20ChIP-seq&status=released$ -Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Homo%20sapiens&assay_title=TF%20ChIP-seq&status=released$ -Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Homo%20sapiens&assay_title=TF%20ChIP-seq&status=released$ -Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Homo%20sapiens&assay_title=TF%20ChIP-seq&status=released$ -Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Mus%20musculus&assay_title=Histone%20ChIP-seq&status=released$ -Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Mus%20musculus&assay_title=Histone%20ChIP-seq&status=released$ -Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Mus%20musculus&assay_title=Histone%20ChIP-seq&status=released$ -Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Mus%20musculus&assay_title=Histone%20ChIP-seq&status=released$ -Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Mus%20musculus&assay_title=TF%20ChIP-seq&status=released$ -Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Mus%20musculus&assay_title=TF%20ChIP-seq&status=released$ -Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Mus%20musculus&assay_title=TF%20ChIP-seq&status=released$ -Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Mus%20musculus&assay_title=TF%20ChIP-seq&status=released$ Allow: /search/?type=Annotation&accession=ENCSR471KRT&accession=ENCSR461KLY&accession=ENCSR770MVN&accession=ENCSR695LYW$ Allow: /search/?type=Annotation&accession=ENCSR405FRQ&accession=ENCSR216NPK$ +Allow: /series-search/?type=DifferentiationSeries$ +Allow: /series-search/?type=DiseaseSeries$ +Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Homo%20sapiens&assay_title=Histone%20ChIP-seq&assay_title=Mint-ChIP-seq&status=released$ +Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Homo%20sapiens&assay_title=TF%20ChIP-seq&status=released$ +Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Mus%20musculus&assay_title=TF%20ChIP-seq&status=released$ +Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Mus%20musculus&assay_title=Histone%20ChIP-seq&assay_title=Mint-ChIP-seq&status=released$ +Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Caenorhabditis%20elegans&assay_title=TF%20ChIP-seq&assay_title=Mint-ChIP-seq&status=released$ +Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Drosophila%20melanogaster&assay_title=TF%20ChIP-seq&status=released$ +Allow: /brain-matrix/?type=Experiment&status=released&internal_tags=RushAD$ +Allow: /deeply-profiled-uniform-batch-matrix/?type=Experiment&control_type!=*&status=released&replicates.library.biosample.biosample_ontology.term_id=EFO:0002106&replicates.library.biosample.biosample_ontology.term_id=EFO:0001203&replicates.library.biosample.biosample_ontology.term_id=EFO:0006711&replicates.library.biosample.biosample_ontology.term_id=EFO:0002713&replicates.library.biosample.biosample_ontology.term_id=EFO:0002847&replicates.library.biosample.biosample_ontology.term_id=EFO:0002074&replicates.library.biosample.biosample_ontology.term_id=EFO:0001200&replicates.library.biosample.biosample_ontology.term_id=EFO:0009747&replicates.library.biosample.biosample_ontology.term_id=EFO:0002824&replicates.library.biosample.biosample_ontology.term_id=CL:0002327&replicates.library.biosample.biosample_ontology.term_id=CL:0002618&replicates.library.biosample.biosample_ontology.term_id=EFO:0002784&replicates.library.biosample.biosample_ontology.term_id=EFO:0001196&replicates.library.biosample.biosample_ontology.term_id=EFO:0001187&replicates.library.biosample.biosample_ontology.term_id=EFO:0002067&replicates.library.biosample.biosample_ontology.term_id=EFO:0001099&replicates.library.biosample.biosample_ontology.term_id=EFO:0002819&replicates.library.biosample.biosample_ontology.term_id=EFO:0009318&replicates.library.biosample.biosample_ontology.term_id=EFO:0001086&replicates.library.biosample.biosample_ontology.term_id=EFO:0007950&replicates.library.biosample.biosample_ontology.term_id=EFO:0003045&replicates.library.biosample.biosample_ontology.term_id=EFO:0003042&replicates.library.biosample.internal_tags=Deeply%20Profiled$ +Allow: /deeply-profiled-matrix/?type=Experiment&control_type!=*&status=released&replicates.library.biosample.biosample_ontology.term_id=EFO:0002106&replicates.library.biosample.biosample_ontology.term_id=EFO:0001203&replicates.library.biosample.biosample_ontology.term_id=EFO:0006711&replicates.library.biosample.biosample_ontology.term_id=EFO:0002713&replicates.library.biosample.biosample_ontology.term_id=EFO:0002847&replicates.library.biosample.biosample_ontology.term_id=EFO:0002074&replicates.library.biosample.biosample_ontology.term_id=EFO:0001200&replicates.library.biosample.biosample_ontology.term_id=EFO:0009747&replicates.library.biosample.biosample_ontology.term_id=EFO:0002824&replicates.library.biosample.biosample_ontology.term_id=CL:0002327&replicates.library.biosample.biosample_ontology.term_id=CL:0002618&replicates.library.biosample.biosample_ontology.term_id=EFO:0002784&replicates.library.biosample.biosample_ontology.term_id=EFO:0001196&replicates.library.biosample.biosample_ontology.term_id=EFO:0001187&replicates.library.biosample.biosample_ontology.term_id=EFO:0002067&replicates.library.biosample.biosample_ontology.term_id=EFO:0001099&replicates.library.biosample.biosample_ontology.term_id=EFO:0002819&replicates.library.biosample.biosample_ontology.term_id=EFO:0009318&replicates.library.biosample.biosample_ontology.term_id=EFO:0001086&replicates.library.biosample.biosample_ontology.term_id=EFO:0007950&replicates.library.biosample.biosample_ontology.term_id=EFO:0003045&replicates.library.biosample.biosample_ontology.term_id=EFO:0003042$ +Allow: /degron-matrix/?type=Experiment&control_type!=*&status=released&internal_tags=Degron$ +Allow: /human-donor-matrix/?type=Experiment&control_type!=*&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&biosample_ontology.classification=tissue&status=released&config=HumanDonorMatrix$ +Allow: /human-donor-matrix/?type=Experiment&control_type!=*&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&status=released&config=HumanDonorMatrix&config=HumanDonorMatrix&biosample_ontology.classification=primary+cell$ +Allow: /human-donor-matrix/?type=Experiment&control_type!=*&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&status=released&config=HumanDonorMatrix&biosample_ontology.classification=tissue&biosample_ontology.classification=primary+cell$ +Allow: /encore-matrix/?type=Experiment&status=released&internal_tags=ENCORE$ +Allow: /stem-cell-matrix/?type=Experiment&replicates.library.biosample.donor.accession=ENCDO222AAA&status=released&control_type!=*$ +Allow: /immune-cells/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&biosample_ontology.cell_slims=hematopoietic+cell&biosample_ontology.classification=primary+cell&control_type!=*&status!=replaced&status!=revoked&status!=archived&biosample_ontology.system_slims=immune+system&biosample_ontology.system_slims=circulatory+system&config=immune$ +Allow: /single-cell/?type=Experiment&assay_slims=Single+cell&status=released&replicates.library.biosample.donor.organism.scientific_name=Homo%20sapiens$ +Allow: /single-cell/?type=FunctionalCharacterizationExperiment&assay_slims=Single+cell&status=released$ +Allow: /single-cell/?type=SingleCellRnaSeries&status=released$ +Allow: /single-cell/?type=Annotation&annotation_type=cell+type+annotation&status=released$ +Allow: /search/?type=Annotation&encyclopedia_version=current&annotation_type=candidate+Cis-Regulatory+Elements&annotation_type=chromatin+state&annotation_type=representative+DNase+hypersensitivity+sites&status=released$ +Allow: /functional-characterization-matrix/?type=FunctionalCharacterizationExperiment&type=FunctionalCharacterizationSeries&type=TransgenicEnhancerExperiment&config=FunctionalCharacterization&datapoint=false&control_type!=*&status=released$ From d22f59398e76c44aab4cbc59337d6672775b6093 Mon Sep 17 00:00:00 2001 From: stuartmiyasato Date: Tue, 18 Jun 2024 14:08:29 -0700 Subject: [PATCH 2/4] Update robots.txt --- src/encoded/static/robots.txt | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/src/encoded/static/robots.txt b/src/encoded/static/robots.txt index 8b89c0fcfe8..7efbfbd55ae 100644 --- a/src/encoded/static/robots.txt +++ b/src/encoded/static/robots.txt @@ -52,6 +52,8 @@ Disallow: /mouse-development-matrix Disallow: /mouse-development-matrix/ Disallow: /functional-characterization-matrix Disallow: /functional-characterization-matrix/ +Disallow: /human-donor-matrix +Disallow: /human-donor-matrix/ Allow: /encode-software/?type=Software Allow: /region-search/ Allow: /rnaget/ @@ -75,6 +77,7 @@ Allow: /summary/?type=Experiment&replicates.library.biosample.donor.organism.sci Allow: /summary/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Drosophila+melanogaster$ Allow: /summary/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Caenorhabditis+elegans$ Allow: /series-search/?type=OrganismDevelopmentSeries$ +Allow: /series-search/?type=OrganismDevelopmentSeries&status=released Allow: /series-search/?type=TreatmentTimeSeries$ Allow: /series-search/?type=TreatmentConcentrationSeries$ Allow: /series-search/?type=ReplicationTimingSeries$ @@ -82,18 +85,20 @@ Allow: /series-search/?type=GeneSilencingSeries$ Allow: /search/?type=Annotation$ Allow: /search/?type=Annotation&encyclopedia_version=ENCODE+v5$ Allow: /search/?type=Annotation&encyclopedia_version=ENCODE+v6$ +Allow: /search/?type=Annotation&encyclopedia_version=current&annotation_type=imputation&status=released Allow: /report/?type=Annotation$ Allow: /report/?type=Annotation&encyclopedia_version=ENCODE+v5$ Allow: /report/?type=Annotation&encyclopedia_version=ENCODE+v6$ Allow: /matrix/?type=Annotation$ +Allow: /matrix/?type=Annotation&annotation_type!=imputation&status=released Allow: /matrix/?type=Annotation&encyclopedia_version=ENCODE+v5$ Allow: /matrix/?type=Annotation&encyclopedia_version=ENCODE+v6$ Allow: /matrix/?type=Annotation&encyclopedia_version=ENCODE+v5&annotation_type=candidate+Cis-Regulatory+Elements$ Allow: /matrix/?type=Annotation&encyclopedia_version=ENCODE+v6&annotation_type=candidate+Cis-Regulatory+Elements$ Allow: /search/?type=AntibodyLot&status=released$ Allow: /entex-matrix/?type=Experiment&status=released&internal_tags=ENTEx$ -Allow: /reference-epigenome-matrix/?type=Experiment&related_series.@type=ReferenceEpigenome&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens$ -Allow: /reference-epigenome-matrix/?type=Experiment&related_series.@type=ReferenceEpigenome&replicates.library.biosample.donor.organism.scientific_name=Mus+musculus$ +Allow: /reference-epigenome-matrix/?type=Experiment&related_series.@type=ReferenceEpigenome&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&status=released$ +Allow: /reference-epigenome-matrix/?type=Experiment&related_series.@type=ReferenceEpigenome&replicates.library.biosample.donor.organism.scientific_name=Mus+musculus&status=released$ Allow: /matrix/?type=Experiment&status=released&internal_tags=ENCORE$ Allow: /mouse-development-matrix/?type=Experiment&status=released&related_series.@type=OrganismDevelopmentSeries&replicates.library.biosample.organism.scientific_name=Mus+musculus$ Allow: /search/?type=Annotation&accession=ENCSR471KRT&accession=ENCSR461KLY&accession=ENCSR770MVN&accession=ENCSR695LYW$ @@ -107,7 +112,7 @@ Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.orga Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Caenorhabditis%20elegans&assay_title=TF%20ChIP-seq&assay_title=Mint-ChIP-seq&status=released$ Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Drosophila%20melanogaster&assay_title=TF%20ChIP-seq&status=released$ Allow: /brain-matrix/?type=Experiment&status=released&internal_tags=RushAD$ -Allow: /deeply-profiled-uniform-batch-matrix/?type=Experiment&control_type!=*&status=released&replicates.library.biosample.biosample_ontology.term_id=EFO:0002106&replicates.library.biosample.biosample_ontology.term_id=EFO:0001203&replicates.library.biosample.biosample_ontology.term_id=EFO:0006711&replicates.library.biosample.biosample_ontology.term_id=EFO:0002713&replicates.library.biosample.biosample_ontology.term_id=EFO:0002847&replicates.library.biosample.biosample_ontology.term_id=EFO:0002074&replicates.library.biosample.biosample_ontology.term_id=EFO:0001200&replicates.library.biosample.biosample_ontology.term_id=EFO:0009747&replicates.library.biosample.biosample_ontology.term_id=EFO:0002824&replicates.library.biosample.biosample_ontology.term_id=CL:0002327&replicates.library.biosample.biosample_ontology.term_id=CL:0002618&replicates.library.biosample.biosample_ontology.term_id=EFO:0002784&replicates.library.biosample.biosample_ontology.term_id=EFO:0001196&replicates.library.biosample.biosample_ontology.term_id=EFO:0001187&replicates.library.biosample.biosample_ontology.term_id=EFO:0002067&replicates.library.biosample.biosample_ontology.term_id=EFO:0001099&replicates.library.biosample.biosample_ontology.term_id=EFO:0002819&replicates.library.biosample.biosample_ontology.term_id=EFO:0009318&replicates.library.biosample.biosample_ontology.term_id=EFO:0001086&replicates.library.biosample.biosample_ontology.term_id=EFO:0007950&replicates.library.biosample.biosample_ontology.term_id=EFO:0003045&replicates.library.biosample.biosample_ontology.term_id=EFO:0003042&replicates.library.biosample.internal_tags=Deeply%20Profiled$ +Allow: /deeply-profiled-uniform-batch-matrix/?type=Experiment&control_type!=*&status=released&replicates.library.biosample.biosample_ontology.term_id=EFO:0002106&replicates.library.biosample.biosample_ontology.term_id=EFO:0001203&replicates.library.biosample.biosample_ontology.term_id=EFO:0006711&replicates.library.biosample.biosample_ontology.term_id=EFO:0002713&replicates.library.biosample.biosample_ontology.term_id=EFO:0002847&replicates.library.biosample.biosample_ontology.term_id=EFO:0002074&replicates.library.biosample.biosample_ontology.term_id=EFO:0001200&replicates.library.biosample.biosample_ontology.term_id=EFO:0009747&replicates.library.biosample.biosample_ontology.term_id=EFO:0002824&replicates.library.biosample.biosample_ontology.term_id=CL:0002327&replicates.library.biosample.biosample_ontology.term_id=CL:0002618&replicates.library.biosample.biosample_ontology.term_id=EFO:0002784&replicates.library.biosample.biosample_ontology.term_id=EFO:0001196&replicates.library.biosample.biosample_ontology.term_id=EFO:0001187&replicates.library.biosample.biosample_ontology.term_id=EFO:0002067&replicates.library.biosample.biosample_ontology.term_id=EFO:0001099&replicates.library.biosample.biosample_ontology.term_id=EFO:0002819&replicates.library.biosample.biosample_ontology.term_id=EFO:0009318&replicates.library.biosample.biosample_ontology.term_id=EFO:0001086&replicates.library.biosample.biosample_ontology.term_id=EFO:0007950&replicates.library.biosample.biosample_ontology.term_id=EFO:0003045&replicates.library.biosample.biosample_ontology.term_id=EFO:0003042&replicates.library.biosample.ontology_term.term_id=EFO:0003042&internal_tags=Deeply%20Profiled Allow: /deeply-profiled-matrix/?type=Experiment&control_type!=*&status=released&replicates.library.biosample.biosample_ontology.term_id=EFO:0002106&replicates.library.biosample.biosample_ontology.term_id=EFO:0001203&replicates.library.biosample.biosample_ontology.term_id=EFO:0006711&replicates.library.biosample.biosample_ontology.term_id=EFO:0002713&replicates.library.biosample.biosample_ontology.term_id=EFO:0002847&replicates.library.biosample.biosample_ontology.term_id=EFO:0002074&replicates.library.biosample.biosample_ontology.term_id=EFO:0001200&replicates.library.biosample.biosample_ontology.term_id=EFO:0009747&replicates.library.biosample.biosample_ontology.term_id=EFO:0002824&replicates.library.biosample.biosample_ontology.term_id=CL:0002327&replicates.library.biosample.biosample_ontology.term_id=CL:0002618&replicates.library.biosample.biosample_ontology.term_id=EFO:0002784&replicates.library.biosample.biosample_ontology.term_id=EFO:0001196&replicates.library.biosample.biosample_ontology.term_id=EFO:0001187&replicates.library.biosample.biosample_ontology.term_id=EFO:0002067&replicates.library.biosample.biosample_ontology.term_id=EFO:0001099&replicates.library.biosample.biosample_ontology.term_id=EFO:0002819&replicates.library.biosample.biosample_ontology.term_id=EFO:0009318&replicates.library.biosample.biosample_ontology.term_id=EFO:0001086&replicates.library.biosample.biosample_ontology.term_id=EFO:0007950&replicates.library.biosample.biosample_ontology.term_id=EFO:0003045&replicates.library.biosample.biosample_ontology.term_id=EFO:0003042$ Allow: /degron-matrix/?type=Experiment&control_type!=*&status=released&internal_tags=Degron$ Allow: /human-donor-matrix/?type=Experiment&control_type!=*&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&biosample_ontology.classification=tissue&status=released&config=HumanDonorMatrix$ From ea49f728b343a5098344d6c36e24fac5ef9ef387 Mon Sep 17 00:00:00 2001 From: stuartmiyasato Date: Thu, 20 Jun 2024 15:12:43 -0700 Subject: [PATCH 3/4] Update robots.txt --- src/encoded/static/robots.txt | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/encoded/static/robots.txt b/src/encoded/static/robots.txt index 7efbfbd55ae..713deb1a1b7 100644 --- a/src/encoded/static/robots.txt +++ b/src/encoded/static/robots.txt @@ -58,6 +58,7 @@ Allow: /encode-software/?type=Software Allow: /region-search/ Allow: /rnaget/ Allow: /encyclopedia/ +Allow: /search/?type=Cart&status=listed&status=released Allow: /search/?type=Experiment$ Allow: /search/?type=Experiment&status=released$ Allow: /search/?type=Experiment&control_type!=*&status=released&perturbed=false$ @@ -65,12 +66,14 @@ Allow: /search/?type=FunctionalCharacterizationExperiment$ Allow: /search/?type=TransgenicEnhancerExperiment$ Allow: /search/?type=FunctionalCharacterizationExperiment&control_type!=*&audit.WARNING.category!=lacking+processed+data$ Allow: /search/?type=FunctionalCharacterizationExperiment&control_type!=*$ +Allow: /search/?type=FunctionalCharacterizationExperiment&type=FunctionalCharacterizationSeries&type=TransgenicEnhancerExperiment&config=FunctionalCharacterization&datapoint=false&control_type!=*&status=released Allow: /report/?type=Experiment$ Allow: /report/?type=Experiment&status=released$ Allow: /matrix/?type=Experiment$ Allow: /matrix/?type=Experiment&status=released$ Allow: /matrix/?type=Experiment&control_type!=*&status=released&perturbed=false$ Allow: /summary/?type=Experiment$ +Allow: /summary/?type=Experiment&control_type!=*&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&status=released Allow: /summary/?type=Experiment&status=released$ Allow: /summary/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens$ Allow: /summary/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Mus+musculus$ @@ -85,6 +88,7 @@ Allow: /series-search/?type=GeneSilencingSeries$ Allow: /search/?type=Annotation$ Allow: /search/?type=Annotation&encyclopedia_version=ENCODE+v5$ Allow: /search/?type=Annotation&encyclopedia_version=ENCODE+v6$ +Allow: /search/?type=Annotation&encyclopedia_version=current&status=released Allow: /search/?type=Annotation&encyclopedia_version=current&annotation_type=imputation&status=released Allow: /report/?type=Annotation$ Allow: /report/?type=Annotation&encyclopedia_version=ENCODE+v5$ @@ -97,6 +101,8 @@ Allow: /matrix/?type=Annotation&encyclopedia_version=ENCODE+v5&annotation_type=c Allow: /matrix/?type=Annotation&encyclopedia_version=ENCODE+v6&annotation_type=candidate+Cis-Regulatory+Elements$ Allow: /search/?type=AntibodyLot&status=released$ Allow: /entex-matrix/?type=Experiment&status=released&internal_tags=ENTEx$ +Allow: /reference-epigenome-matrix/?type=Experiment&control_type!=*&related_series.@type=ReferenceEpigenome&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&status=released +Allow: /reference-epigenome-matrix/?type=Experiment&control_type!=*&related_series.@type=ReferenceEpigenome&replicates.library.biosample.donor.organism.scientific_name=Mus+musculus&status=released Allow: /reference-epigenome-matrix/?type=Experiment&related_series.@type=ReferenceEpigenome&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&status=released$ Allow: /reference-epigenome-matrix/?type=Experiment&related_series.@type=ReferenceEpigenome&replicates.library.biosample.donor.organism.scientific_name=Mus+musculus&status=released$ Allow: /matrix/?type=Experiment&status=released&internal_tags=ENCORE$ @@ -121,6 +127,7 @@ Allow: /human-donor-matrix/?type=Experiment&control_type!=*&replicates.library.b Allow: /encore-matrix/?type=Experiment&status=released&internal_tags=ENCORE$ Allow: /stem-cell-matrix/?type=Experiment&replicates.library.biosample.donor.accession=ENCDO222AAA&status=released&control_type!=*$ Allow: /immune-cells/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&biosample_ontology.cell_slims=hematopoietic+cell&biosample_ontology.classification=primary+cell&control_type!=*&status!=replaced&status!=revoked&status!=archived&biosample_ontology.system_slims=immune+system&biosample_ontology.system_slims=circulatory+system&config=immune$ +Allow: /immune-cells/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&biosample_ontology.cell_slims=hematopoietic+cell&biosample_ontology.classification=primary+cell&control_type!=*&status=released&biosample_ontology.system_slims=immune+system&biosample_ontology.system_slims=circulatory+system&config=immune Allow: /single-cell/?type=Experiment&assay_slims=Single+cell&status=released&replicates.library.biosample.donor.organism.scientific_name=Homo%20sapiens$ Allow: /single-cell/?type=FunctionalCharacterizationExperiment&assay_slims=Single+cell&status=released$ Allow: /single-cell/?type=SingleCellRnaSeries&status=released$ From 57247b5a988ee2bb1e0c2a0d5ca49e5e79738448 Mon Sep 17 00:00:00 2001 From: stuartmiyasato Date: Wed, 26 Jun 2024 09:56:20 -0700 Subject: [PATCH 4/4] Update robots.txt --- src/encoded/static/robots.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/encoded/static/robots.txt b/src/encoded/static/robots.txt index 713deb1a1b7..96d731f093b 100644 --- a/src/encoded/static/robots.txt +++ b/src/encoded/static/robots.txt @@ -118,7 +118,7 @@ Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.orga Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Caenorhabditis%20elegans&assay_title=TF%20ChIP-seq&assay_title=Mint-ChIP-seq&status=released$ Allow: /chip-seq-matrix/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Drosophila%20melanogaster&assay_title=TF%20ChIP-seq&status=released$ Allow: /brain-matrix/?type=Experiment&status=released&internal_tags=RushAD$ -Allow: /deeply-profiled-uniform-batch-matrix/?type=Experiment&control_type!=*&status=released&replicates.library.biosample.biosample_ontology.term_id=EFO:0002106&replicates.library.biosample.biosample_ontology.term_id=EFO:0001203&replicates.library.biosample.biosample_ontology.term_id=EFO:0006711&replicates.library.biosample.biosample_ontology.term_id=EFO:0002713&replicates.library.biosample.biosample_ontology.term_id=EFO:0002847&replicates.library.biosample.biosample_ontology.term_id=EFO:0002074&replicates.library.biosample.biosample_ontology.term_id=EFO:0001200&replicates.library.biosample.biosample_ontology.term_id=EFO:0009747&replicates.library.biosample.biosample_ontology.term_id=EFO:0002824&replicates.library.biosample.biosample_ontology.term_id=CL:0002327&replicates.library.biosample.biosample_ontology.term_id=CL:0002618&replicates.library.biosample.biosample_ontology.term_id=EFO:0002784&replicates.library.biosample.biosample_ontology.term_id=EFO:0001196&replicates.library.biosample.biosample_ontology.term_id=EFO:0001187&replicates.library.biosample.biosample_ontology.term_id=EFO:0002067&replicates.library.biosample.biosample_ontology.term_id=EFO:0001099&replicates.library.biosample.biosample_ontology.term_id=EFO:0002819&replicates.library.biosample.biosample_ontology.term_id=EFO:0009318&replicates.library.biosample.biosample_ontology.term_id=EFO:0001086&replicates.library.biosample.biosample_ontology.term_id=EFO:0007950&replicates.library.biosample.biosample_ontology.term_id=EFO:0003045&replicates.library.biosample.biosample_ontology.term_id=EFO:0003042&replicates.library.biosample.ontology_term.term_id=EFO:0003042&internal_tags=Deeply%20Profiled +Allow: /deeply-profiled-uniform-batch-matrix/?type=Experiment&control_type!=*&status=released&replicates.library.biosample.biosample_ontology.term_id=EFO:0002106&replicates.library.biosample.biosample_ontology.term_id=EFO:0001203&replicates.library.biosample.biosample_ontology.term_id=EFO:0006711&replicates.library.biosample.biosample_ontology.term_id=EFO:0002713&replicates.library.biosample.biosample_ontology.term_id=EFO:0002847&replicates.library.biosample.biosample_ontology.term_id=EFO:0002074&replicates.library.biosample.biosample_ontology.term_id=EFO:0001200&replicates.library.biosample.biosample_ontology.term_id=EFO:0009747&replicates.library.biosample.biosample_ontology.term_id=EFO:0002824&replicates.library.biosample.biosample_ontology.term_id=CL:0002327&replicates.library.biosample.biosample_ontology.term_id=CL:0002618&replicates.library.biosample.biosample_ontology.term_id=EFO:0002784&replicates.library.biosample.biosample_ontology.term_id=EFO:0001196&replicates.library.biosample.biosample_ontology.term_id=EFO:0001187&replicates.library.biosample.biosample_ontology.term_id=EFO:0002067&replicates.library.biosample.biosample_ontology.term_id=EFO:0001099&replicates.library.biosample.biosample_ontology.term_id=EFO:0002819&replicates.library.biosample.biosample_ontology.term_id=EFO:0009318&replicates.library.biosample.biosample_ontology.term_id=EFO:0001086&replicates.library.biosample.biosample_ontology.term_id=EFO:0007950&replicates.library.biosample.biosample_ontology.term_id=EFO:0003045&replicates.library.biosample.biosample_ontology.term_id=EFO:0003042&replicates.library.biosample.internal_tags=Deeply%20Profiled Allow: /deeply-profiled-matrix/?type=Experiment&control_type!=*&status=released&replicates.library.biosample.biosample_ontology.term_id=EFO:0002106&replicates.library.biosample.biosample_ontology.term_id=EFO:0001203&replicates.library.biosample.biosample_ontology.term_id=EFO:0006711&replicates.library.biosample.biosample_ontology.term_id=EFO:0002713&replicates.library.biosample.biosample_ontology.term_id=EFO:0002847&replicates.library.biosample.biosample_ontology.term_id=EFO:0002074&replicates.library.biosample.biosample_ontology.term_id=EFO:0001200&replicates.library.biosample.biosample_ontology.term_id=EFO:0009747&replicates.library.biosample.biosample_ontology.term_id=EFO:0002824&replicates.library.biosample.biosample_ontology.term_id=CL:0002327&replicates.library.biosample.biosample_ontology.term_id=CL:0002618&replicates.library.biosample.biosample_ontology.term_id=EFO:0002784&replicates.library.biosample.biosample_ontology.term_id=EFO:0001196&replicates.library.biosample.biosample_ontology.term_id=EFO:0001187&replicates.library.biosample.biosample_ontology.term_id=EFO:0002067&replicates.library.biosample.biosample_ontology.term_id=EFO:0001099&replicates.library.biosample.biosample_ontology.term_id=EFO:0002819&replicates.library.biosample.biosample_ontology.term_id=EFO:0009318&replicates.library.biosample.biosample_ontology.term_id=EFO:0001086&replicates.library.biosample.biosample_ontology.term_id=EFO:0007950&replicates.library.biosample.biosample_ontology.term_id=EFO:0003045&replicates.library.biosample.biosample_ontology.term_id=EFO:0003042$ Allow: /degron-matrix/?type=Experiment&control_type!=*&status=released&internal_tags=Degron$ Allow: /human-donor-matrix/?type=Experiment&control_type!=*&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&biosample_ontology.classification=tissue&status=released&config=HumanDonorMatrix$