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Change http to https for ncbi.nlm.nih.gov server
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dkandrov committed Sep 30, 2016
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24 changes: 12 additions & 12 deletions data/DBXRefRegistry.txt
@@ -1,6 +1,6 @@
#db_xref_ID|db_xref_PageLink|db_xref_FileLink|db_xref_Comment
#Official site: http://www.ncbi.nlm.nih.gov/genbank/collab/db_xref
AceView/WormGenes|http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?exdb=AceView&db=worm&term=%1||AceView Worm Genome
AceView/WormGenes|https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?exdb=AceView&db=worm&term=%1||AceView Worm Genome

AFTOL|http://aftol1.biology.duke.edu/pub/primers/getPrimersByAFTOLID?aftol_id=%1||Assembling the Fungal Tree of Life

Expand Down Expand Up @@ -42,19 +42,19 @@ CABRI|||Common Access to Biological Resources and Information Project

CCAP|||Culture Collection of Algae and Protozoa

CDD|http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=%1||Conserved Domain Database
CDD|https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=%1||Conserved Domain Database

CGD|http://www.candidagenome.org/cgi-bin/locus.pl?dbid=%1||Candida Genome Database

CCDS|http://www.ncbi.nlm.nih.gov/projects/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=%1&ORGANISM=0&BUILDS=CURRENTBUILDS||The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality.
CCDS|https://www.ncbi.nlm.nih.gov/projects/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=%1&ORGANISM=0&BUILDS=CURRENTBUILDS||The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality.

dbEST|http://www.ncbi.nlm.nih.gov/sites/entrez?db=nucest&term=%1&pmfilter_MDatLimit=10+Years||EST database maintained at the NCBI.
dbEST|https://www.ncbi.nlm.nih.gov/sites/entrez?db=nucest&term=%1&pmfilter_MDatLimit=10+Years||EST database maintained at the NCBI.

dbProbe|http://www.ncbi.nlm.nih.gov/sites/entrez?db=probe&cmd=search&term=%1||NCBI Probe database Public registry of nucleic acid reagents
dbProbe|https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe&cmd=search&term=%1||NCBI Probe database Public registry of nucleic acid reagents

dbSNP|http://www.ncbi.nlm.nih.gov/sites/entrez?db=snp&cmd=search&term=%1||Variation database maintained at the NCBI.
dbSNP|https://www.ncbi.nlm.nih.gov/sites/entrez?db=snp&cmd=search&term=%1||Variation database maintained at the NCBI.

dbSTS|http://www.ncbi.nlm.nih.gov/sites/entrez?db=unists&cmd=search&term=%1||STS database maintained at the NCBI.
dbSTS|https://www.ncbi.nlm.nih.gov/sites/entrez?db=unists&cmd=search&term=%1||STS database maintained at the NCBI.

dictyBase|http://dictybase.org/db/cgi-bin/gene_page.pl?primary_id=%1||Dictyostelium genome database

Expand Down Expand Up @@ -82,9 +82,9 @@ GDB|||Human Genome Database accession numbers

GeneDB|http://www.genedb.org/genedb/Dispatcher?formType=navBar&organism=All%3A*&name=%1&desc=yes||Curated gene database for Schizosaccharomyces pombe, Leishmania major and Trypanosoma brucei

GeneID|http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=%1||Entrez Gene Database (replaces NCBI Locus Link)
GeneID|https://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=%1||Entrez Gene Database (replaces NCBI Locus Link)

GI|http://www.ncbi.nlm.nih.gov/sites/gquery?term=%1||GenInfo identifier, used as a unique sequence identifier for nucleotide and proteins
GI|https://www.ncbi.nlm.nih.gov/sites/gquery?term=%1||GenInfo identifier, used as a unique sequence identifier for nucleotide and proteins

GO|||Gene Ontology Database identifier

Expand Down Expand Up @@ -130,11 +130,11 @@ LocusID|||NCBI LocusLink ID **Discontinued March 2005

MaizeGDB|||Maize Genome Database unique identifiers

MedGen|http://www.ncbi.nlm.nih.gov/medgen/?term=%1||Human Medical Genetics
MedGen|https://www.ncbi.nlm.nih.gov/medgen/?term=%1||Human Medical Genetics

MGI||| Mouse Genome Informatics

MIM|http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=%1|| Mendelian Inheritance in Man numbers
MIM|https://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=%1|| Mendelian Inheritance in Man numbers

miRBase|http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?acc=%1||miRBase is the new home of microRNA data on the web, providing data previously accessible from the miRNA Registry.

Expand Down Expand Up @@ -224,7 +224,7 @@ UniProtKB/Swiss-Prot|http://www.uniprot.org/uniprot/%1|http://www.uniprot.org/un

UniProtKB/TrEMBL|http://www.uniprot.org/uniprot/%1|http://www.uniprot.org/uniprot/%1.txt|section of the UniProt Knowledgebase, containing computationally analysed records waiting for full manual annotation

UniSTS|http://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=%1||NCBI UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments.
UniSTS|https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=%1||NCBI UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments.

UNITE|||Molecular database for the identification of fungi

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6 changes: 3 additions & 3 deletions src/corelibs/U2Core/src/tasks/LoadRemoteDocumentTask.cpp
Expand Up @@ -48,9 +48,9 @@

namespace U2 {

const QString EntrezUtils::NCBI_ESEARCH_URL("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=%1&term=%2&retmax=%3&tool=UGENE");
const QString EntrezUtils::NCBI_ESUMMARY_URL("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=%1&id=%2&tool=UGENE");
const QString EntrezUtils::NCBI_EFETCH_URL("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=%1&id=%2&retmode=text&rettype=%3&tool=UGENE");
const QString EntrezUtils::NCBI_ESEARCH_URL("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=%1&term=%2&retmax=%3&tool=UGENE");
const QString EntrezUtils::NCBI_ESUMMARY_URL("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=%1&id=%2&tool=UGENE");
const QString EntrezUtils::NCBI_EFETCH_URL("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=%1&id=%2&retmode=text&rettype=%3&tool=UGENE");
const QString EntrezUtils::NCBI_DB_NUCLEOTIDE("nucleotide");
const QString EntrezUtils::NCBI_DB_PROTEIN("protein");

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