cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5007992.v2
title: Distant Supervision of Structured Biomedical Data Based on Text Surrounding Figure References

description: Data accompanying the paper entitled "Resources for Distant Supervision of Structured Biomedical Data Based on Text Surrounding Figure References". <br>This fileset consists of the following archives:<br>* <b>nxml</b> - INTACT open source articles processed in this paper downloaded from PMC.* <b>train+test</b> - Training and testing data for SciDT in TSV form. The articles forming this small corpus are derived from open source papers indexed in the Pathway Logic database developed by SRI International. * <b>scidt_bioc</b> - data fully processed by the SciDT pipeline and saved in BioC format* <b>scidt_fries_bioc_tsv</b> - data fully processed by the SciDT pipeline and saved in TSV format* <b>biopax</b> - All open access data from INTACT reformatted into biopax and preserving figure-level meta data. * <b>w3c_annotations</b> - A linked data representation connecting Biopax Evidence instances to Web Annotations embedded in the published, open access research articles. <br>* <b>amr_data </b>- Abstract meaning representation data for 1963 separate fragments derived from INTACT figure legends, converted to 1961 linked data elements using AMR-LD (https://github.com/BMKEG/amr-ld). <br>
DOI: 10.6084/m9.figshare.5007965.v1
title: demo data for the error

description: demo data for the error for waters data
DOI: 10.6084/m9.figshare.5007992.v3
title: Molecular Interaction Evidence Fragment Corpus

description: This file set showcases the first presentation of an annotated text corpus of 'evidence fragments' from biomedical papers. These are short passages of text from the results sections of papers that describe the goals, methods, results and interpretations of experiments that are reported as figures in biomedical articles. These figures typically provide the evidence and justification for any underlying scientific explanation or argument being explored in any given paper. Moreover, these fragments describe the specific findings of experimental studies and therefore comprise the 'raw material' of investigative scientific work. It is for that reason that we prioritize them within this corpus. <br><br>The file set should be considered as consisting of two parts: (1) a single archive of annotated text fragments forming the 'Molecular Interaction Evidence Fragment Corpus' (intact_evidence_fragment_corpus_07-25-17.tar.gz); and (2) other files provided for provenance and reproducibility. <br><br><b>The 'Molecular Interaction Evidence Fragment Corpus'<br></b><br>This gzipped tar archive forms the initial preparation of distant learning data corpus where we develop a method to link text to data. Here we use references to figure labels ('Fig 2a', etc) to identify (A) excerpts from the results sections of papers describing the goals, methods, results and interpretations of experiments showcased in those figures. We call these passages 'evidence fragments' and are contained in *.ttl files that use an OWL-enabled version of the National Library of Medicine's BioC standoff annotation format (http://bioc.sourceforge.org/) with additional relations from the SPAR ontologies (http://sparontologies.net/) to link these fragments to figure references. (B) We also use these same figure references to anchor manually-curated INTACT data records where noted (http://www.ebi.ac.uk/intact/). We restricted our analysis to papers from the PMC open access subset. <br><b>Provenance Data Files.<br></b><b><br></b>We provide a set of files for the purposes of provenance and reproducibility. This includes the following subsets of papers:<br>* <b>nxml</b> - INTACT open source articles processed in this paper downloaded from PMC.* <b>train+test</b> - Training and testing data for SciDT in TSV form. The articles forming this small corpus are derived from open source papers indexed in the Pathway Logic database developed by SRI International. * <b>scidt_bioc</b> - data fully processed by the SciDT pipeline and saved in BioC format<br>http://purl.org/ske/ro/semsci17 points to a research object (http://www.researchobject.org) that links to the software used to generate this data. <br>
DOI: 10.6084/m9.figshare.5007773
title: Salmonella Enteritidis, chicks & poults data

description: Data associated with 575 Salmonella Enteritidis genomes submitted to NCBI under BioProject PRJNA343897
DOI: 10.6084/m9.figshare.5007785
title: Entity Relatedness Test Dataset

description: The entity relatedness problem refers to the question of computing the relationship paths that better describe the connectivity between a given entity pair. This dataset supports the evaluation of approaches that address the entity relatedness problem. It covers two familiar domains, music and movies, and uses data available in IMDb and last.fm, which are popular reference datasets in these domains. The dataset contains 20 entity pairs from each of these domains and, for each entity pair, a ranked list with 50 relationship paths. It also contains entity ratings and property relevance scores for the entities and properties used in the paths.
DOI: 10.6084/m9.figshare.5007746
title: Experimental data -- Nonlinear mode interaction in equal-leg angle struts susceptible to cellular buckling

description: A total number of 10 compression tests were conducted on thin-walled equal-leg angle struts made of cold-formed steel.
DOI: 10.6084/m9.figshare.5007773.v1
title: Salmonella Enteritidis, chicks & poults data

description: Data associated with 575 Salmonella Enteritidis genomes submitted to NCBI under BioProject PRJNA343897
DOI: 10.6084/m9.figshare.5007737
title: Drinking water treatment plant - Fungal ITS sequencing FASTAQ

description: Raw Illumina MiSeq fastq files and mapping file used for demultiplexing in QIIME<br>
DOI: 10.6084/m9.figshare.5007743
title: Drinking water treatment plant - 16S sequencing FASTAQ

description: Raw FASTQ files and mapping file for demultiplexing in QIIME<br>
DOI: 10.6084/m9.figshare.5007746.v1
title: Experimental data -- Nonlinear mode interaction in equal-leg angle struts susceptible to cellular buckling

description: A total number of 10 compression tests were conducted on thin-walled equal-leg angle struts made of cold-formed steel.
DOI: 10.6084/m9.figshare.5006492
title: L1400_2.xlsx

description: Experimental data for test specimen L1400_2
DOI: 10.6084/m9.figshare.5007992.v4
title: Molecular Interaction Evidence Fragment Corpus

description: This file set showcases the first presentation of an annotated text corpus of 'evidence fragments' from biomedical papers. These are short passages of text from the results sections of papers that describe the goals, methods, results and interpretations of experiments that are reported as figures in biomedical articles. These figures typically provide the evidence and justification for any underlying scientific explanation or argument being explored in any given paper. Moreover, these fragments describe the specific findings of experimental studies and therefore comprise the 'raw material' of investigative scientific work. It is for that reason that we prioritize them within this corpus. <br><br>The file set should be considered as consisting of two parts: (1) a single archive of annotated text fragments forming the 'Molecular Interaction Evidence Fragment Corpus' (intact_evidence_fragment_corpus_07-25-17.tar.gz); and (2) other files provided for provenance and reproducibility. <br><br><b>The 'Molecular Interaction Evidence Fragment Corpus'<br></b><br>This gzipped tar archive forms the initial preparation of distant learning data corpus where we develop a method to link text to data. Here we use references to figure labels ('Fig 2a', etc) to identify (A) excerpts from the results sections of papers describing the goals, methods, results and interpretations of experiments showcased in those figures. We call these passages 'evidence fragments' and are contained in *.ttl files that use an OWL-enabled version of the National Library of Medicine's BioC standoff annotation format (http://bioc.sourceforge.org/) with additional relations from the SPAR ontologies (http://sparontologies.net/) to link these fragments to figure references. (B) We also use these same figure references to anchor manually-curated INTACT data records where noted (http://www.ebi.ac.uk/intact/). We restricted our analysis to papers from the PMC open access subset. <br><b>Provenance Data Files.<br></b><b><br></b>We provide a set of files for the purposes of provenance and reproducibility. This includes the following subsets of papers:<br>* <b>nxml</b> - INTACT open source articles processed in this paper downloaded from PMC.* <b>train+test</b> - Training and testing data for SciDT in TSV form. The articles forming this small corpus are derived from open source papers indexed in the Pathway Logic database developed by SRI International. * <b>scidt_bioc</b> - data fully processed by the SciDT pipeline and saved in BioC format* <b>gannt</b> - 'gantt' charts for each paper that show the distribution of evidence fragments over clauses in the results sections of papers. <br>http://purl.org/ske/ro/semsci17 points to a research object (http://www.researchobject.org) that links to the software used to generate this data. <br>
DOI: 10.6084/m9.figshare.5006492.v1
title: L1400_2.xlsx

description: Experimental data for test specimen L1400_2
DOI: 10.6084/m9.figshare.5007737.v1
title: Drinking water treatment plant - Fungal ITS sequencing FASTAQ

description: Raw Illumina MiSeq fastq files and mapping file used for demultiplexing in QIIME<br>
DOI: 10.6084/m9.figshare.5007743.v1
title: Drinking water treatment plant - 16S sequencing FASTAQ

description: Raw FASTQ files and mapping file for demultiplexing in QIIME<br>
DOI: 10.6084/m9.figshare.5006054
title: Cleaned-up cyanobacterial genome assemblies from Cornet et al. Consensus assessment of the contamination level of publicly available cyanobacterial genomes.

description: This archive contains cleaned-up versions of 440 cyanobacterial genomes, in which the foreign (i.e., non-cyanobacterial) segments have been masked with N's.
DOI: 10.6084/m9.figshare.5006084
title: Question Answering Data

description: A large scale dataset for complex Question Answering.<br>
DOI: 10.6084/m9.figshare.5006090
title: VoID Resource

description: Machine readable description of the dataset.<br>
DOI: 10.6084/m9.figshare.5005985
title: Spruyt & De Houwer (submitted). On the automaticity of relational stimulus processing: Footnote 1 (RST study 2)

description: Zip folder with raw data files of the second unpublished RST study referred to in Footnote 1.
DOI: 10.6084/m9.figshare.5005985.v1
title: Spruyt & De Houwer (submitted). On the automaticity of relational stimulus processing: Footnote 1 (RST study 2)

description: Zip folder with raw data files of the second unpublished RST study referred to in Footnote 1.
DOI: 10.6084/m9.figshare.5005961
title: Download scripts (database links) for Cornet et al. Consensus assessment of the contamination level of publicly available cyanobacterial genomes.

description: This archive contains two download scripts that are basically collection of FTP links to public genome databases.<br>- Cyanobacteria.sh: 440 cyanobacterial genome assemblies- curated-ensembl-30.sh: 27,762 prokaryotic genomes from Ensembl 30 that are mostly contamination-free.
DOI: 10.6084/m9.figshare.5006084.v2
title: Question Answering Data

description: A large scale dataset for complex Question Answering<br>
DOI: 10.6084/m9.figshare.5006054.v1
title: Cleaned-up cyanobacterial genome assemblies from Cornet et al. How often publicly available genomes are contaminated? Cyanobacteria as a case study.

description: This archive contains cleaned-up versions of 440 cyanobacterial genomes, in which the foreign (i.e., non-cyanobacterial) segments have been masked with N's.
DOI: 10.6084/m9.figshare.5005952
title: Collecting information and NCBI GenBank accession numbers for COI sequences of Chelonibia testudinaria

description: Collecting information and NCBI GenBank accession numbers of the Chelonibia testudinaria barnacles for which we generated mitochondrial COI sequences<br>
DOI: 10.6084/m9.figshare.5006054.v3
title: Cleaned-up cyanobacterial genome assemblies from Cornet et al. Consensus assessment of the contamination level of publicly available cyanobacterial genomes.

description: This archive contains cleaned-up versions of 440 cyanobacterial genomes, in which the foreign (i.e., non-cyanobacterial) segments have been masked with N's.
DOI: 10.6084/m9.figshare.5006084.v3
title: Question Answering Data

description: A large scale dataset for complex Question Answering<br>
DOI: 10.6084/m9.figshare.5005952.v1
title: Collecting information and NCBI GenBank accession numbers for COI sequences of Chelonibia testudinaria

description: Collecting information and NCBI GenBank accession numbers of the Chelonibia testudinaria barnacles for which we generated mitochondrial COI sequences<br>
DOI: 10.6084/m9.figshare.5006054.v2
title: Cleaned-up cyanobacterial genome assemblies from Cornet et al. Consensus assessment of the contamination level of 440 publicly available cyanobacterial genomes.

description: This archive contains cleaned-up versions of 440 cyanobacterial genomes, in which the foreign (i.e., non-cyanobacterial) segments have been masked with N's.
DOI: 10.6084/m9.figshare.5005940
title: Spruyt & De Houwer (submitted). On the automaticity of relational stimulus processing: Footnote 1 (RST study 1)

description: Zip folder with raw data files of the first unpublished RST study referred to in Footnote 1.
DOI: 10.6084/m9.figshare.5005940.v1
title: Spruyt & De Houwer (submitted). On the automaticity of relational stimulus processing: Footnote 1 (RST study 1)

description: Zip folder with raw data files of the first unpublished RST study referred to in Footnote 1.
DOI: 10.6084/m9.figshare.5005961.v2
title: Download scripts (database links) for Cornet et al. Consensus assessment of the contamination level of 440 publicly available cyanobacterial genomes.

description: This archive contains two download scripts that are basically collection of ftp links to public genome databases.<br>- Cyanobacteria.sh: 440 cyanobacterial genome assemblies- curated-ensembl-30.sh: 27,762 prokaryotic genomes from Ensembl 30 that are mostly contamination-free.
DOI: 10.6084/m9.figshare.5006084.v4
title: Question Answering Data

description: A large scale dataset for complex Question Answering<br>
DOI: 10.6084/m9.figshare.5006084.v5
title: Question Answering Data

description: A large scale dataset for complex Question Answering<br>
DOI: 10.6084/m9.figshare.5005961.v3
title: Download scripts (database links) for Cornet et al. Consensus assessment of the contamination level of 440 publicly available cyanobacterial genomes.

description: This archive contains two download scripts that are basically collection of FTP links to public genome databases.<br>- Cyanobacteria.sh: 440 cyanobacterial genome assemblies- curated-ensembl-30.sh: 27,762 prokaryotic genomes from Ensembl 30 that are mostly contamination-free.
DOI: 10.6084/m9.figshare.5006084.v6
title: Question Answering Data

description: A large scale dataset for complex Question Answering<br>
DOI: 10.6084/m9.figshare.5005961.v4
title: Download scripts (database links) for Cornet et al. Consensus assessment of the contamination level of 440 publicly available cyanobacterial genomes.

description: This archive contains two download scripts that are basically collection of FTP links to public genome databases.<br>- Cyanobacteria.sh: 440 cyanobacterial genome assemblies- curated-ensembl-30.sh: 27,762 prokaryotic genomes from Ensembl 30 that are mostly contamination-free.
DOI: 10.6084/m9.figshare.5005655
title: Taxonomy and phylogeny of <i>Lineus torquatus</i> and allies (Nemertea, Lineidae) with descriptions of a new genus and a new cryptic species

description: The heteronemertean genus <i>Lineus</i> Sowerby, 1806 has been badly in need of revision because of its apparent non-monophyly. In this paper, we focus on <i>Lineus torquatus</i> Coe, 1901, one of the heteronemertean species that occur commonly in waters around the North Pacific, as well as a few other allied species distributed in the western North Pacific, including <i>Lineus alborostratus</i> Takakura, 1898 and <i>Cerebratulus montgomeryi</i> Coe, 1901. Based on phylogenetic analyses using <i>16S</i>, <i>COI</i>, <i>28S</i>, <i>18S</i>, and <i>H3</i> gene and <i>ITS</i> sequences, we detected a well-supported clade comprised of heteronemerteans with a frontal white band on the head, to which we add <i>Kulikovia</i> gen. nov. This genus is nested within a more comprehensive, highly supported clade, here named the <i>Siphonenteron</i>-clade, which contains <i>Tenuilineus bicolour</i> (Verrill, 1892), <i>Lineus flavescens</i> Coe, 1905, <i>Siphonenteron bilineatum</i> (Renier, 1804), <i>S.</i> cf. <i>bilineatum</i>, <i>Lineus</i> cf. <i>caputornatus</i>, and <i>Lineus</i> sp. from Guam. Our analyses confirmed the presence of a cryptic species of what was formerly known as the cherry-red and reddish forms of <i>Lineus torquatus</i>, herein described as <i>Kulikovia manchenkoi</i> sp. nov. based on some external characters, internal morphology, and the four genetic markers (<i>COI</i>, <i>16S</i>, <i>H3</i>, and <i>ITS</i>). In contrast to the species pair <i>K. torquata</i>–<i>K. manchenkoi</i>, the reddish form of <i>K. alborostrata</i> does not differ genetically from the typical form of this species. The significance of the external and internal characters for distinguishing cryptic species is discussed. http://zoobank.org/urn:lsid:zoobank.org:pub:9BECBC60-9C82-48EC-AD36-FC564D82A5BChttp://zoobank.org/urn:lsid:zoobank.org:act:D02B2339-4F65-4517-9B13-DD4AAB0C55C5http://zoobank.org/urn:lsid:zoobank.org:act:8D239B62-E655-4721-90F0-A4944DD8A3C7
DOI: 10.6084/m9.figshare.5005655.v1
title: Taxonomy and phylogeny of <i>Lineus torquatus</i> and allies (Nemertea, Lineidae) with descriptions of a new genus and a new cryptic species

description: The heteronemertean genus <i>Lineus</i> Sowerby, 1806 has been badly in need of revision because of its apparent non-monophyly. In this paper, we focus on <i>Lineus torquatus</i> Coe, 1901, one of the heteronemertean species that occur commonly in waters around the North Pacific, as well as a few other allied species distributed in the western North Pacific, including <i>Lineus alborostratus</i> Takakura, 1898 and <i>Cerebratulus montgomeryi</i> Coe, 1901. Based on phylogenetic analyses using <i>16S</i>, <i>COI</i>, <i>28S</i>, <i>18S</i>, and <i>H3</i> gene and <i>ITS</i> sequences, we detected a well-supported clade comprised of heteronemerteans with a frontal white band on the head, to which we add <i>Kulikovia</i> gen. nov. This genus is nested within a more comprehensive, highly supported clade, here named the <i>Siphonenteron</i>-clade, which contains <i>Tenuilineus bicolour</i> (Verrill, 1892), <i>Lineus flavescens</i> Coe, 1905, <i>Siphonenteron bilineatum</i> (Renier, 1804), <i>S.</i> cf. <i>bilineatum</i>, <i>Lineus</i> cf. <i>caputornatus</i>, and <i>Lineus</i> sp. from Guam. Our analyses confirmed the presence of a cryptic species of what was formerly known as the cherry-red and reddish forms of <i>Lineus torquatus</i>, herein described as <i>Kulikovia manchenkoi</i> sp. nov. based on some external characters, internal morphology, and the four genetic markers (<i>COI</i>, <i>16S</i>, <i>H3</i>, and <i>ITS</i>). In contrast to the species pair <i>K. torquata</i>–<i>K. manchenkoi</i>, the reddish form of <i>K. alborostrata</i> does not differ genetically from the typical form of this species. The significance of the external and internal characters for distinguishing cryptic species is discussed. http://zoobank.org/urn:lsid:zoobank.org:pub:9BECBC60-9C82-48EC-AD36-FC564D82A5BChttp://zoobank.org/urn:lsid:zoobank.org:act:D02B2339-4F65-4517-9B13-DD4AAB0C55C5http://zoobank.org/urn:lsid:zoobank.org:act:8D239B62-E655-4721-90F0-A4944DD8A3C7
DOI: 10.6084/m9.figshare.5005961.v6
title: Download scripts (database links) for Cornet et al. Consensus assessment of the contamination level of publicly available cyanobacterial genomes.

description: This archive contains two download scripts that are basically collection of FTP links to public genome databases.<br>- Cyanobacteria.sh: 440 cyanobacterial genome assemblies- curated-ensembl-30.sh: 27,762 prokaryotic genomes from Ensembl 30 that are mostly contamination-free.
DOI: 10.6084/m9.figshare.5006084.v7
title: Question Answering Data

description: A large scale dataset for complex Question Answering<br>
DOI: 10.6084/m9.figshare.5005643
title: Original search strategy, the full list of items to be coded, and pre-planned analyses to explain heterogeneity for “Does prosocial behavior increase well-being in controlled experiments? A systematic review and a meta-analysis” Prospero pre-report

description: Original search strategy, the full list of itemst to be coded and pre-planned analyses to explain heterogeneity for "Does prosocial behavior increase well-being in controlled experiments? A systematic review and a meta-analysis<br>
DOI: 10.6084/m9.figshare.5006084.v9
title: Question Answering Data

description: A large scale dataset for complex Question Answering.<br>
DOI: 10.6084/m9.figshare.5005961.v5
title: Download scripts (database links) for Cornet et al. Consensus assessment of the contamination level of 440 publicly available cyanobacterial genomes.

description: This archive contains two download scripts that are basically collection of FTP links to public genome databases.<br>- Cyanobacteria.sh: 440 cyanobacterial genome assemblies- curated-ensembl-30.sh: 27,762 prokaryotic genomes from Ensembl 30 that are mostly contamination-free.
DOI: 10.6084/m9.figshare.5006084.v8
title: Question Answering Data

description: A large scale dataset for complex Question Answering.<br>
DOI: 10.6084/m9.figshare.5005643.v1
title: Original search strategy, the full list of items to be coded, and pre-planned analyses to explain heterogeneity for “Does prosocial behavior increase well-being in controlled experiments? A systematic review and a meta-analysis” Prospero pre-report

description: Original search strategy, the full list of itemst to be coded and pre-planned analyses to explain heterogeneity for "Does prosocial behavior increase well-being in controlled experiments? A systematic review and a meta-analysis<br>
DOI: 10.6084/m9.figshare.5005634.v1
title: Intraspecific killing behaviour of canids: how dingoes kill dingoes

description: Intraspecific conflict is an important process structuring carnivore populations. However, few data are available describing the precise mode of killing used by carnivores, especially medium-sized carnivores that can exhibit behaviours typically associated with either smaller or larger species. From records of free-ranging Australian dingoes killed during intraspecific fighting, we describe the types, location and frequency of injuries sustained, to assist in identifying killing behaviours common to medium-sized carnivores, or mesopredators. Observed injuries included superficial minor cuts and other wounds, deep punctures (bite marks or holes), severe lacerations to internal organs, tissue bruising and crushing, mutilation of muscle tissue, perforation of the chest and abdominal cavities, and a variety of bone fractures. The dingoes in this study predominately died from gross internal haemorrhaging caused by crushing bites coupled with vigorous shaking to the head, throat, neck and ventral chest areas. Our data demonstrate that dingoes used a ‘bite and shake’ mode of killing. This killing behaviour is dissimilar to those exhibited by large carnivores, but is consistent with behaviours shown by other medium-sized carnivores.
DOI: 10.6084/m9.figshare.5005508
title: Spruyt & De Houwer (submitted). On the automaticity of relational stimulus processing: Experiment 1

description: Zip folder with raw data files of Experiment 1