cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.16595167
title: Supporting data for: Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic

description: Supporting data for "Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic".

This archive consists of:



v1 



 variant_calls_and_benchmarks.tar.gz



deepsomatic-training-set

deepsomatic-multicancer-model-benchmark

orthogonal-technology-benchmark

orthogonal-tools-benchmark

somatic-variant-calling-outputs



deepsomatic_v1.8.0

strelka2

clairs_ssrs

clairs_v0.2.0

varnet







v2



 scripts_and_commands.tar.gz



deepsomatic.wdl                

bwa_mem2.wdl

minimap2_ubam.wdl            

minimap2_fastq.wdl

pbmm2.wdl            

vcf_intersection.py

vcf_to_bed_v4.py

tumor_purity_titration.sh

normal_purity_titration.sh        

split_bam_normal.sh    

split_bam_tumor.sh

generate_high_confidence_regions.sh    

clairs.sh                        

strelka2.sh                

deepvariant_hybrid.sh            

mutational_matrix_generation.sh    

mutational_signature_analysis.sh        

wambam.sh

sompy.sh
DOI: 10.5281/zenodo.16650334
title: Supporting data for: Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic

description: Supporting data for "Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic".

This archive consists of:



v1 



 variant_calls_and_benchmarks.tar.gz



deepsomatic-training-set

deepsomatic-multicancer-model-benchmark

orthogonal-technology-benchmark

orthogonal-tools-benchmark

somatic-variant-calling-outputs



deepsomatic_v1.8.0

strelka2

clairs_ssrs

clairs_v0.2.0

varnet







v2



 scripts_and_commands.tar.gz



deepsomatic.wdl                

bwa_mem2.wdl

minimap2_ubam.wdl            

minimap2_fastq.wdl

pbmm2.wdl            

vcf_intersection.py

vcf_to_bed_v4.py

tumor_purity_titration.sh

normal_purity_titration.sh        

split_bam_normal.sh    

split_bam_tumor.sh

generate_high_confidence_regions.sh    

clairs.sh                        

strelka2.sh                

deepvariant_hybrid.sh            

mutational_matrix_generation.sh    

mutational_signature_analysis.sh        

wambam.sh

sompy.sh
DOI: 10.15468/dl.jsunux
title: Occurrence Download

description: A dataset containing 16862 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Iris germanica"
 ]
}

 The dataset includes 16862 records from 576 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0081823-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.afskr3
title: Occurrence Download

description: A dataset containing 202371 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Trebouxiophyceae"
 ]
}

 The dataset includes 202371 records from 955 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010998-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc110591785
title: Persepolis Fortification Aramaic Text 261, PFAT 261

description: [Text Description:] Administrative text with seals PFS 0142; PFATS 0024* ❧ [Text or Publication Number Note:] PFAT 261, Bowman 261 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Aramaic ❧ [Physical Object Description:] Clay tablet with ink inscription. Seal impressions PFS 0142 on obverse; PFATS 0024* on reverse, flat edge. ❧ [Physical Object Note:] Damage on upper edge, round edge
DOI: 10.25549/inscriptifact-ouc110591795
title: Persepolis Fortification Aramaic Text 262, PFAT 262

description: [Text Description:] Administrative text with seals PFATS 0001s; PFATS 0274s; PFUTS 0109s ❧ [Text or Publication Number Note:] PFAT 262, Bowman 262 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Aramaic ❧ [Physical Object Description:] Clay tablet with ink inscription. Seal impressions PFATS 0001s on upper edge; PFATS 0274s on reverse; PFUTS 0109s on bottom edge. ❧ [Physical Object Note:] Damage on flat edge
DOI: 10.25549/jrbm-c91-1289
title: Kankai ibun, vol. 7, 1807

description: Kankai ibun, [1807], volume 7 = Description and travel of circumnavigation of seas, [1807], volume 7 = 環海 異聞 七 文化 4. Volume seven of a manuscript by Gentaku Ōtsuki and Kōkyō Shimura who drew from four Japanese fishermen the story of their voyage around the world during repeated interviews. The Kankai Ibun is an account of their journey when they were sent off-course en route to the capital, Edo. The fishermen were rescued by a Russian ship and taken to late 18th / early 19th century Europe and, most especially, Russia.; The cargo ship, Wakamiyamaru, left from the port of Ishimaki in Sendai-han, today’s Miyagi Prefecture, in Japan carrying rice and lumber with 16 crew members for Edo, today’s Tokyo, on November 27th, 1793. Shipwrecked and drifted in the Pacific Ocean for half a year, they finally landed in one of the islands of the Andreanof Islands, a part of the Aleutian Islands on May 10th, 1794. They were transferred to Irkutsk by Russians where they stayed until the spring of 1803. They were then called in by Alexander I of Russia to St. Petersburg where they stayed from April to June in 1803, and from where they started their journey back home. They were included in the Rezanov mission on the first Russian global circumnavigation by a ship Nadezhda. It took them 16 months to reach the port of Nagasaki, Japan in September, 1804 since they left in June, 1803. Of the sixteen, five crewmen got on board. Four returned home in Sendai; one, who had become an interpreter, returned to Russia with Rezanov.
DOI: 10.25549/inscriptifact-ouc110591793
title: Persepolis Fortification Aramaic Text 262, PFAT 262

description: [Text Description:] Administrative text with seals PFATS 0001s; PFATS 0274s; PFUTS 0109s ❧ [Text or Publication Number Note:] PFAT 262, Bowman 262 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Aramaic ❧ [Physical Object Description:] Clay tablet with ink inscription. Seal impressions PFATS 0001s on upper edge; PFATS 0274s on reverse; PFUTS 0109s on bottom edge. ❧ [Physical Object Note:] Damage on flat edge
DOI: 10.25549/jrbm-c91-1317
title: Kankai ibun, vol. 7, 1807

description: Kankai ibun, [1807], volume 7 = Description and travel of circumnavigation of seas, [1807], volume 7 = 環海 異聞 七 文化 4. Volume seven of a manuscript by Gentaku Ōtsuki and Kōkyō Shimura who drew from four Japanese fishermen the story of their voyage around the world during repeated interviews. The Kankai Ibun is an account of their journey when they were sent off-course en route to the capital, Edo. The fishermen were rescued by a Russian ship and taken to late 18th / early 19th century Europe and, most especially, Russia.; The cargo ship, Wakamiyamaru, left from the port of Ishimaki in Sendai-han, today’s Miyagi Prefecture, in Japan carrying rice and lumber with 16 crew members for Edo, today’s Tokyo, on November 27th, 1793. Shipwrecked and drifted in the Pacific Ocean for half a year, they finally landed in one of the islands of the Andreanof Islands, a part of the Aleutian Islands on May 10th, 1794. They were transferred to Irkutsk by Russians where they stayed until the spring of 1803. They were then called in by Alexander I of Russia to St. Petersburg where they stayed from April to June in 1803, and from where they started their journey back home. They were included in the Rezanov mission on the first Russian global circumnavigation by a ship Nadezhda. It took them 16 months to reach the port of Nagasaki, Japan in September, 1804 since they left in June, 1803. Of the sixteen, five crewmen got on board. Four returned home in Sendai; one, who had become an interpreter, returned to Russia with Rezanov.
DOI: 10.25549/inscriptifact-ouc110591771
title: Persepolis Fortification Aramaic Text 261, PFAT 261

description: [Text Description:] Administrative text with seals PFS 0142; PFATS 0024* ❧ [Text or Publication Number Note:] PFAT 261, Bowman 261 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Aramaic ❧ [Physical Object Description:] Clay tablet with ink inscription. Seal impressions PFS 0142 on obverse; PFATS 0024* on reverse, flat edge. ❧ [Physical Object Note:] Damage on upper edge, round edge
DOI: 10.25549/inscriptifact-ouc110591788
title: Persepolis Fortification Aramaic Text 262, PFAT 262

description: [Text Description:] Administrative text with seals PFATS 0001s; PFATS 0274s; PFUTS 0109s ❧ [Text or Publication Number Note:] PFAT 262, Bowman 262 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Aramaic ❧ [Physical Object Description:] Clay tablet with ink inscription. Seal impressions PFATS 0001s on upper edge; PFATS 0274s on reverse; PFUTS 0109s on bottom edge. ❧ [Physical Object Note:] Damage on flat edge
DOI: 10.25549/jrbm-c91-443
title: Kankai ibun, vol. 8, 1807

description: Kankai ibun, [1807], volume 8 = Description and travel of circumnavigation of seas, [1807], volume 8 = 環海 異聞 八 文化 4. Volume eight of a manuscript by Gentaku Ōtsuki and Kōkyō Shimura who drew from four Japanese fishermen the story of their voyage around the world during repeated interviews. The Kankai Ibun is an account of their journey when they were sent off-course en route to the capital, Edo. The fishermen were rescued by a Russian ship and taken to late 18th / early 19th century Europe and, most especially, Russia.; The cargo ship, Wakamiyamaru, left from the port of Ishimaki in Sendai-han, today’s Miyagi Prefecture, in Japan carrying rice and lumber with 16 crew members for Edo, today’s Tokyo, on November 27th, 1793. Shipwrecked and drifted in the Pacific Ocean for half a year, they finally landed in one of the islands of the Andreanof Islands, a part of the Aleutian Islands on May 10th, 1794. They were transferred to Irkutsk by Russians where they stayed until the spring of 1803. They were then called in by Alexander I of Russia to St. Petersburg where they stayed from April to June in 1803, and from where they started their journey back home. They were included in the Rezanov mission on the first Russian global circumnavigation by a ship Nadezhda. It took them 16 months to reach the port of Nagasaki, Japan in September, 1804 since they left in June, 1803. Of the sixteen, five crewmen got on board. Four returned home in Sendai; one, who had become an interpreter, returned to Russia with Rezanov.
DOI: 10.15468/dl.mc6uxm
title: Occurrence Download

description: A dataset containing 1598 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON((-115.08336 35.98365,-115.06483 35.9529,-115.06398 35.93858,-115.08083 35.92721,-115.08842 35.92257,-115.09937 35.92005,-115.10189 35.9251,-115.10863 35.92552,-115.10737 35.91794,-115.11453 35.91836,-115.12001 35.91583,-115.12928 35.9171,-115.13559 35.91752,-115.15371 35.91878,-115.16171 35.9112,-115.16087 35.90572,-115.15539 35.90362,-115.14697 35.90699,-115.13728 35.90741,-115.12759 35.90783,-115.11832 35.90362,-115.10695 35.90235,-115.09726 35.89772,-115.07157 35.90614,-115.06525 35.90783,-115.05767 35.90741,-115.05008 35.90277,-115.04334 35.90404,-115.03365 35.90193,-115.03618 35.89393,-115.0366 35.88635,-115.03913 35.87876,-115.04082 35.87076,-115.04545 35.86865,-115.05724 35.87118,-115.0623 35.87076,-115.06567 35.86528,-115.06946 35.86276,-115.07536 35.85981,-115.07241 35.85517,-115.07325 35.84759,-115.07114 35.84254,-115.08168 35.83411,-115.08715 35.82779,-115.09726 35.83538,-115.10316 35.84633,-115.11285 35.85939,-115.11874 35.86444,-115.12717 35.86276,-115.1377 35.87666,-115.14612 35.88845,-115.15581 35.90193,-115.16255 35.9053,-115.17056 35.90277,-115.16466 35.8973,-115.16382 35.88719,-115.15918 35.87876,-115.14865 35.87371,-115.14528 35.86823,-115.1377 35.85096,-115.12464 35.85391,-115.11495 35.84633,-115.11369 35.83917,-115.0981 35.82105,-115.09726 35.81516,-115.09136 35.81095,-115.0842 35.81137,-115.07957 35.80758,-115.04461 35.808,-115.04419 35.85054,-115.00206 35.85138,-114.99911 35.93942,-114.99195 35.94743,-114.99237 35.9588,-114.98269 35.95711,-114.98353 35.97649,-114.99448 35.97649,-114.99406 35.99671,-115.04671 35.99882,-115.04756 35.98407,-115.08336 35.98365))"
 ]
}

 The dataset includes 1598 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027484-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc1sto1607419
title: InscriptiFact -- an image database of inscriptions and artifacts

description: The InscriptiFact Collection is designed to allow access via the Internet to high-resolution images of ancient inscriptions and artifacts, primarily from the Near Eastern and Mediterranean Worlds. The targeted inscriptions constitute some of the world’s earliest written records, which are mostly housed in a number of international museums and libraries, as well as field projects where inscriptions still remain in situ. Included, for example, are, selected Dead Sea Scrolls; cuneiform tablets from Mesopotamia, Persia, Canaan and Egypt; early Jewish papyri from Egypt; lapidary inscriptions, primarily from Jordan, Lebanon and Cyprus; inscriptions on a variety of hard media (e.g., ostraca, copper, semi-precious stones, jar handles) mostly written in early Canaanite, Phoenician, Hebrew, Aramaic, Ammonite and Edomite; and much more. These ancient texts are foundational documents that serve as a point of reference for Judaism, Christianity, Islam and the cultures out of which they emerged. The name "InscriptiFact" is intended to convey the concept of a scholarly archive based on "facts" about "inscriptions" and "artifacts." West Semitic Research Project (WSRP) under the auspices of the University of Southern California (USC) is broadly acknowledged as a leader in the application of photographic and digital technologies to capture and analyze data of ancient texts. The West Semitic Research image archive now contains approximately 1,500,000 images. Important! Search terms with more than one word or number need to be enclosed in quotation marks.Guide to Searching InscriptiFact
DOI: 10.25549/inscriptifact-ouc110591787
title: Persepolis Fortification Aramaic Text 261, PFAT 261

description: [Text Description:] Administrative text with seals PFS 0142; PFATS 0024* ❧ [Text or Publication Number Note:] PFAT 261, Bowman 261 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Aramaic ❧ [Physical Object Description:] Clay tablet with ink inscription. Seal impressions PFS 0142 on obverse; PFATS 0024* on reverse, flat edge. ❧ [Physical Object Note:] Damage on upper edge, round edge
DOI: 10.25549/inscriptifact-ouc110591768
title: Persepolis Fortification Aramaic Text 261, PFAT 261

description: [Text Description:] Administrative text with seals PFS 0142; PFATS 0024* ❧ [Text or Publication Number Note:] PFAT 261, Bowman 261 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Aramaic ❧ [Physical Object Description:] Clay tablet with ink inscription. Seal impressions PFS 0142 on obverse; PFATS 0024* on reverse, flat edge. ❧ [Physical Object Note:] Damage on upper edge, round edge
DOI: 10.25549/jrbm-c91-1272
title: Kankai ibun, vol. 7, 1807

description: Kankai ibun, [1807], volume 7 = Description and travel of circumnavigation of seas, [1807], volume 7 = 環海 異聞 七 文化 4. Volume seven of a manuscript by Gentaku Ōtsuki and Kōkyō Shimura who drew from four Japanese fishermen the story of their voyage around the world during repeated interviews. The Kankai Ibun is an account of their journey when they were sent off-course en route to the capital, Edo. The fishermen were rescued by a Russian ship and taken to late 18th / early 19th century Europe and, most especially, Russia.; The cargo ship, Wakamiyamaru, left from the port of Ishimaki in Sendai-han, today’s Miyagi Prefecture, in Japan carrying rice and lumber with 16 crew members for Edo, today’s Tokyo, on November 27th, 1793. Shipwrecked and drifted in the Pacific Ocean for half a year, they finally landed in one of the islands of the Andreanof Islands, a part of the Aleutian Islands on May 10th, 1794. They were transferred to Irkutsk by Russians where they stayed until the spring of 1803. They were then called in by Alexander I of Russia to St. Petersburg where they stayed from April to June in 1803, and from where they started their journey back home. They were included in the Rezanov mission on the first Russian global circumnavigation by a ship Nadezhda. It took them 16 months to reach the port of Nagasaki, Japan in September, 1804 since they left in June, 1803. Of the sixteen, five crewmen got on board. Four returned home in Sendai; one, who had become an interpreter, returned to Russia with Rezanov.
DOI: 10.5255/ukda-sn-7594-4
title: Scottish Health Survey, 2013
title: Scottish Health Survey, 1995-
title: SHeS

description: The &lt;i&gt;Scottish Health Survey, 2013&lt;/i&gt; was the ninth survey in the series, designed to provide data at a national level about the population living in private households in Scotland. Since its inception in 1995, the SHeS interview has included a second stage follow-up visit from a survey nurse to collect biological samples and measures. Between 2012 and 2015, specially trained interviewers are taking many of the measurements and samples, previously collected by nurses, from a sub-sample of adult participants.&lt;br&gt;
&lt;br&gt;For the fourth edition (January 2019), corrections have been made to the class variables (sclass, &lt;span style="color: inherit; font-size: inherit;"&gt;scallx and &lt;/span&gt;scallxg2) contained in the individual 2013 data file and the individual socio-economic group variable (SEG) has been added; in addition, the combined 2012-2013 data file was replaced with an updated version.&lt;br&gt;
 The &lt;I&gt;Scottish Health Survey&lt;/I&gt; (SHeS) series was established in 1995. Commissioned by the Scottish Government Health Directorates, the series provides regular information on aspects of the public's health and factors related to health which cannot be obtained from other sources. The SHeS series was designed to:&lt;ul&gt;&lt;li&gt;estimate the prevalence of particular health conditions in Scotland;&lt;/li&gt;&lt;li&gt;estimate the prevalence of certain risk factors associated with these health conditions and to document the pattern of related health behaviours;&lt;/li&gt;&lt;li&gt;look at differences between regions and between subgroups of the population in the extent of their having these particular health conditions or risk factors, and to make comparisons with other national statistics for Scotland and England;&lt;/li&gt;&lt;li&gt;monitor trends in the population's health over time;&lt;/li&gt;&lt;li&gt;make a major contribution to monitoring progress towards health targets.&lt;/li&gt;&lt;/ul&gt;Each survey in the series includes a set of core questions and measurements (height and weight and, if applicable, blood pressure, waist circumference, urine and saliva samples), plus modules of questions on specific health conditions that vary from year to year. Each year the core sample has also been augmented by an additional boosted sample for children. Since 2008 NHS Health Boards have also had the opportunity to boost the number of adult interviews carried out in their area.  &lt;br&gt;
&lt;br&gt;
The Scottish Government &lt;a href="http://www.scotland.gov.uk/Topics/Statistics/Browse/Health/scottish-health-survey" title="Scottish Health Survey"&gt;Scottish Health Survey&lt;/a&gt; webpages contain further information about the series, including latest news and publications. &lt;br&gt;
&lt;br&gt;
DOI: 10.5255/ukda-sn-8356-2
title: Annual Population Survey, April 2017 - March 2018
DOI: 10.25549/inscriptifact-ouc110596410
title: Persepolis Fortification Aramaic Text 340, PFAT 340

description: [Text Description:] Administrative text with seals PFATS 0336?; PFATS 0069*; PFATS 0001s. ❧ [Text or Publication Number Note:] PFAT 340, Bowman 340 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Aramaic ❧ [Physical Object Description:] Clay tablet with ink inscription. Seal impressions PFATS 0336? on upper edge; PFATS 0069* on reverse; PFATS 0001s on bottom edge. ❧ [Physical Object Note:] Damage on flat edge, round edge.
DOI: 10.25549/jrbm-c91-383
title: Kankai ibun, vol. 8, 1807

description: Kankai ibun, [1807], volume 8 = Description and travel of circumnavigation of seas, [1807], volume 8 = 環海 異聞 八 文化 4. Volume eight of a manuscript by Gentaku Ōtsuki and Kōkyō Shimura who drew from four Japanese fishermen the story of their voyage around the world during repeated interviews. The Kankai Ibun is an account of their journey when they were sent off-course en route to the capital, Edo. The fishermen were rescued by a Russian ship and taken to late 18th / early 19th century Europe and, most especially, Russia.; The cargo ship, Wakamiyamaru, left from the port of Ishimaki in Sendai-han, today’s Miyagi Prefecture, in Japan carrying rice and lumber with 16 crew members for Edo, today’s Tokyo, on November 27th, 1793. Shipwrecked and drifted in the Pacific Ocean for half a year, they finally landed in one of the islands of the Andreanof Islands, a part of the Aleutian Islands on May 10th, 1794. They were transferred to Irkutsk by Russians where they stayed until the spring of 1803. They were then called in by Alexander I of Russia to St. Petersburg where they stayed from April to June in 1803, and from where they started their journey back home. They were included in the Rezanov mission on the first Russian global circumnavigation by a ship Nadezhda. It took them 16 months to reach the port of Nagasaki, Japan in September, 1804 since they left in June, 1803. Of the sixteen, five crewmen got on board. Four returned home in Sendai; one, who had become an interpreter, returned to Russia with Rezanov.