(Q38841549)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28400424%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

title

Increased taxon sampling reveals thousands of hidden orthologs in flatworms (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28400424%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28400424%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

José María Martín-Durán

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28400424%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

Joseph F Ryan

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28400424%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

Bruno C. Vellutini

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28400424%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

Kevin Pang

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28400424%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

author name string

José M Martín-Durán

1

1 reference

6 September 2017

11 April 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28400424%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28400424%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

volume

27

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28400424%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

issue

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28400424%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

page(s)

1263-1272

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28400424%20AND%20SRC:MED&resulttype=core&format=json

describes a project that uses

17 March 2020

1 reference

10 June 2022

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&rettype=xml&id=5495077

cites work

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1 reference

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Towards Consensus Gene Ages

9 September 2017

1 reference

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TransRate: reference-free quality assessment of de novo transcriptome assemblies

9 September 2017

1 reference

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Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

PlanMine--a mineable resource of planarian biology and biodiversity

9 September 2017

1 reference

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Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano.

9 September 2017

1 reference

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9 September 2017

Hidden genes in birds.

1 reference

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OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy

9 September 2017

1 reference

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Spiralian phylogeny informs the evolution of microscopic lineages

9 September 2017

1 reference

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SmedGD 2.0: The Schmidtea mediterranea genome database

9 September 2017

1 reference

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Flatworms have lost the right open reading frame kinase 3 gene during evolution

9 September 2017

1 reference

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A Transcriptomic-Phylogenomic Analysis of the Evolutionary Relationships of Flatworms

9 September 2017

1 reference

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Evolutionary analysis of mitogenomes from parasitic and free-living flatworms

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Nuclear genomic signals of the 'microturbellarian' roots of platyhelminth evolutionary innovation

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

The BioGRID interaction database: 2015 update

9 September 2017

1 reference

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Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Platyzoan paraphyly based on phylogenomic data supports a noncoelomate ancestry of spiralia

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

The life cycle of Drosophila orphan genes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

InterProScan 5: genome-scale protein function classification

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

The planarian regeneration transcriptome reveals a shared but temporally shifted regulatory program between opposing head and tail scenarios.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

The genomes of four tapeworm species reveal adaptations to parasitism

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Q&A: what is regeneration, and why look to planarians for answers?

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Pleckstrin homology (PH) like domains - versatile modules in protein-protein interaction platforms

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

A beginner's guide to eukaryotic genome annotation

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Summarizing and correcting the GC content bias in high-throughput sequencing

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Centrosome loss in the evolution of planarians

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Accelerated Profile HMM Searches

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

The draft genome of the carcinogenic human liver fluke Clonorchis sinensis

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Wnt gene loss in flatworms.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

The evolutionary origin of orphan genes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Cestode genomics - progress and prospects for advancing basic and applied aspects of flatworm biology

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Occurrence and abundance of a mariner-like element in freshwater and terrestrial planarians (Platyhelminthes, Tricladida) from southern Brazil

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Homologous over-extension: a challenge for iterative similarity searches

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

BLAST+: architecture and applications

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

The flowering world: a tale of duplications

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

More than just orphans: are taxonomically-restricted genes important in evolution?

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

The evolutionary significance of ancient genome duplications

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

The genome of the blood fluke Schistosoma mansoni

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

HaMStR: profile hidden markov model based search for orthologs in ESTs

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

How confident can we be that orthologs are similar, but paralogs differ?

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Assessing the gene space in draft genomes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

CAIcal: a combined set of tools to assess codon usage adaptation

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Transposable elements and the evolution of regulatory networks

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Orthology and functional conservation in eukaryotes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

On homology searches by protein Blast and the characterization of the age of genes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Improving the specificity of high-throughput ortholog prediction

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Orthologs, paralogs, and evolutionary genomics

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Evolutionary genomics: yeasts accelerate beyond BLAST.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Three classes of C2H2 zinc finger proteins

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

The F-box protein family.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Codon usage tabulated from international DNA sequence databases: status for the year 2000

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Preservation of duplicate genes by complementary, degenerative mutations

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

The use of gene clusters to infer functional coupling

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

A genomic perspective on protein families

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Effective protein sequence comparison

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Distinguishing Homologous from Analogous Proteins

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Basic local alignment search tool

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently "orphan" viral proteins

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

A tight link between orthologs and bidirectional best hits in bacterial and archaeal genomes

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Evolutionary implications of morphogenesis and molecular patterning of the blind gut in the planarian Schmidtea polychroa

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

A map of the protein space--an automatic hierarchical classification of all protein sequences

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

High copy number of highly similar mariner-like transposons in planarian (Platyhelminthe): evidence for a trans-phyla horizontal transfer.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Bidirectional best hits miss many orthologs in duplication-rich clades such as plants and animals

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Functional and evolutionary implications of gene orthology.

22 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Evidence for compensatory evolution of ribosomal proteins in response to rapid divergence of mitochondrial rRNA.

22 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Structure of the planarian central nervous system (CNS) revealed by neuronal cell markers

22 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

The "inverse relationship between evolutionary rate and age of mammalian genes" is an artifact of increased genetic distance with rate of evolution and time of divergence

22 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

A planarian orthopedia homolog is specifically expressed in the branch region of both the mature and regenerating brain.

22 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5495077

Higher-level metazoan relationships: recent progress and remaining questions

22 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1101%2FGR.216226.116

TransRate: reference free quality assessment of de-novo transcriptome assemblies

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1101%2FGR.216226.116

21 January 2018

Identifiers

DOI

10.1101/GR.216226.116

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28400424%20AND%20SRC:MED&resulttype=core&format=json

release_knsp7rwumnfd3p2wyd5xld6d4e

17 March 2020

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/knsp7rwumnfd3p2wyd5xld6d4e

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28400424%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

1 reference