This work aimed to transform raw data in high quality and well organized data for research studies addressing genetics and neurodevelopmental disorders. Information and relations between patients, cnvs, genes, GO terms, and diagnoses where passed through a very demanding quality check analysis before being inserted in the relational database in order to eliminate redundancies and enhance uniformity whenever possible. By using this data, researchers can start their work one step further by querying and identifying data suitable for analysis rather than spent time in tasks related to data cleaning and data pre-processing.

The archive includes copies, compilation code, documentation and temporary data files for the BioDeepTime database.

Deposited files:

Relational database in SQLite format: biodeeptime_sqlite.zip.

Denormalized database in zipped .csv format: biodeeptime_csv.zip

Denormalized database in zipped .parquet (v1.0) format: biodeeptime_parquet.zip.

Denormalized database in .rds (R version 4.0) format: biodeeptime.rds.

Description of tables and columns: biodeeptime.md.

Database schema: schema.pdf.

Synonymy of sources: Synonymy of sources.xlsx.

Change log and known issues: NEWS.md

Compilation files: bdt_compilation.zip

References in .csv format: references.csv

References in .rds format: references.rds

Reference bibtex entries: references.bib

Bchron ages calculated for Neotoma: neotoma_bchron.rds

This repository accompanies the study BioDeepTime: a database of biodiversity time series for modern and fossil assemblages by Smith et al. (In Press).

The Biological Sampling Database (BSD) is an Oracle relational database that is maintained at the NMFS Panama City Laboratory and NOAA NMFS Beaufort Laboratory. Data set includes port samples of reef fish species collected from commercial and recreational fishery landings in the U.S. South Atlantic (NC - FL Keys). The data set serves as an inventory of samples stored at the NMFS Beaufort Laboratory as well as final processed data. Information that may be inlcuded for each sample is trip level information, species, size meansurements, age, sex and reproductive data.

The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis.

A large crowd-sourced dataset for developing natural language interfaces for relational databases. WikiSQL is the dataset released along with our work Seq2SQL: Generating Structured Queries from Natural Language using Reinforcement Learning. Link: https://github.com/salesforce/WikiSQL Notebook: https://colab.research.google.com/drive/1dOTP5Fir04MLDD0nS8YpenwnWp8uG-de?usp=sharing Citation If you use WikiSQL, please cite the following work:

Victor Zhong, Caiming Xiong, and Richard Socher. 2017. Seq2SQL: Generating Structured Queries from Natural Language using Reinforcement Learning.

@article{zhongSeq2SQL2017, author = {Victor Zhong and Caiming Xiong and Richard Socher}, title = {Seq2SQL: Generating Structured Queries from Natural Language using Reinforcement Learning}, journal = {CoRR}, volume = {abs/1709.00103}, year = {2017} } Notes Regarding tokenization and Stanza --- when WikiSQL was written 3-years ago, it relied on Stanza, a CoreNLP python wrapper that has since been deprecated. If you'd still like to use the tokenizer, please use the docker image. We do not anticipate switching to the current Stanza as changes to the tokenizer would render the previous results not reproducible.

LICENSE BSD 3-Clause License

Copyright (c) 2017, Salesforce Research All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

• Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

• Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

• Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Database TSCEvolTree_Aze&2011_GTS2020 is database TSCEvolTree_Aze&2011_CorrJul2018, of anudc:5528 (which see), with stratigraphic ranges now calibrated to timescale GTS2020.
Calibration to GTS2020 employed planktonic foraminifer datums for Neogene of Raffi & others (2020) and for remaining Cenozoic of TimeScale Creator 8.0 (Ogg & others, 2021) after Gradstein & others (2020).

References:
Fordham, B. G., Aze, T., Haller, C., Zehady, A. K., Pearson, P. N., Ogg, J. G., & Wade, B. S. 2018. Future-proofing the Cenozoic macroperforate planktonic foraminifera phylogeny of Aze & others (2011). PLoS ONE 13(10): e0204625.
Gradstein, F. M., Ogg, J. G., Schmitz, M. D., & Ogg, G. M. (Ed.) 2020. A Geologic Time Scale 2020. Elsevier, Amsterdam. 1357 pp.
Ogg, J. G., Ogg, G. M., Gradstein, F. M., Lugowski, A., Ault, A., Zehady, A. K., Chunduru, N. V., Gangi, P., & Ogg, N. 2021. Time Scale Creator. Java software package (Version 8.0). Geologic TimeScale Foundation Inc. https://timescalecreator.org
Raffi, I., Wade, B. S., & Pälike, H. 2020. The Neogene Period. In: Gradstein, F. M., Ogg, J. G., Schmitz, M. D., & Ogg, G. M., Geologic Time Scale 2020. Elsevier, Amsterdam: 1141–1215.

PLBD (Protein Ligand Binding Database) table description XML file

General

The provided ZIP archive contains an XML file "main-database-description.xml" with the description of all tables (VIEWS) that are exposed publicly at the PLBD server (https://plbd.org/). In the XML file, all columns of the visible tables are described, specifying their SQL types, measurement units, semantics, calculation formulae, SQL statements that can be used to generate values in these columns, and publications of the formulae derivations.

The XML file conforms to the published XSD schema created for descriptions of relational databases for specifications of scientific measurement data. The XSD schema ("relational-database_v2.0.0-rc.18.xsd") and all included sub-schemas are provided in the same archive for convenience. All XSD schemas are validated against the "XMLSchema.xsd" schema from the W3C consortium.

The ZIP file contains the excerpt from the files hosted in the https://plbd.org/ at the moment of submission of the PLBD database in the Scientific Data journal, and is provided to conform the journal policies. The current data and schemas should be fetched from the published URIs:

https://plbd.org/
https://plbd.org/doc/db/schemas
https://plbd.org/doc/xml/schemas

Software that is used to generate SQL schemas, RestfulDB metadata and the RestfulDB middleware that allows to publish the databases generated from the XML description on the Web are available at public Subversion repositories:

svn://www.crystallography.net/solsa-database-scripts
svn://saulius-grazulis.lt/restfuldb

Usage

The unpacked ZIP file will create the "db/" directory with the tree layout given below. In addition to the database description file "main-database-description.xml", all XSD schemas necessary for validation of the XML file are provided. On a GNU/Linux operating system with a GNU Make package installed, the XML file validity can be checked by unpacking the ZIP file, entering the unpacked directory, and running 'make distclean; make'. For example, on a Linux Mint distribution, the following commands should work:

unzip main-database-description.zip
cd db/release/v0.10.0/tables/
sh -x dependencies/Linuxmint-20.1/install.sh
make distclean
make

If necessary, additional packages can be installed using the 'install.sh' script in the 'dependencies/' subdirectory corresponding to your operating system. As of the moment of writing, Debian-10 and Linuxmint-20.1 OSes are supported out of the box; similar OSes might work with the same 'install.sh' scripts. The installation scripts require to run package installation command under system administrator privileges, but they use only the standard system package manager, thus they should not put your system at risk. For validation and syntax checking, the 'rxp' and 'xmllint' programs are used.

The log files provided in the "outputs/validation" subdirectory contain validation logs obtained on the system where the XML files were last checked and should indicate validity of the provided XML file against the references schemas.

Layout of the archived file tree

db/
└── release
  └── v0.10.0
    └── tables
      ├── Makeconfig-validate-xml
      ├── Makefile
      ├── Makelocal-validate-xml
      ├── dependencies
      ├── main-database-description.xml
      ├── outputs
      └── schema

The GlycoSuite database (GlycoSuiteDB) is an annotated and curated relational database of glycan structures and is a product of Tyrian Diagnostics Ltd (formerly Proteome Systems Ltd). Currently, the database contains most published O-linked glycans, and N-linked glycans in the literature from the years 1990-2005. For each structure, information is available concerning the glycan type, linkage and anomeric configuration, mass and composition. Detailed information is provided on native and recombinant sources, including tissue and/or cell type, cell line, strain and disease state. Where known, the proteins to which the glycan structures are attached are described, and cross-references to Swiss-Prot/TrEMBL are given if applicable. The database annotations include literature references which are linked to PubMed, and detailed information on the methods used to determine each glycan structure are noted to assess the quality of the structural assignment.

CSRDB is a bioinformatics resource for cereal crops consisting of large-scale datasets of maize and rice and small RNA sequences. The sequences were generated by 454 Life Science sequencing. The small RNA sequences have been mapped to the rice genome and available maize genome sequence and are presented in two genome browser datasets using the Generic Genome Browser. Potential target sequences representing mature mRNA sequences have been predicted using the FASTH software from the Zuker lab. and access to the resulting small RNA target pair (SRTP) dataset has been made available through a mysql based relational database. Within the genome browser the small RNAs have links to the SRTP database that will return a list of potential targets. The SRTP database may also be searched independently using both small RNA and target transcript queries. Data linking and integration is the main focus of this interface and to this aim links are present in the SRTP results pages back to the browser and the SRTP database as well as external sites.

The relationship between aggression and mate choice in mating systems is critical for understanding the evolution and diversification of sexual organisms, and yet remains the subject of vigorous debate. A key challenge is that traditional correlational approaches cannot distinguish underlying mechanisms of social interaction and can indicate misleading positive associations between aggression and mating events. We implement a novel Relational Event Model (REM) incorporating temporal dependencies of events in a social network to study natural reproductive behavior in a lek-breeding system where males gather to display and females visit to evaluate mates, often observing both male courtship displays and fights. We find that fighting is not attractive to females. Indeed, males are less likely to start and more likely to leave fights with females present, plausibly to avoid entanglement in protracted combat cycles arising from emergent social processes that reduce availability to mate. However, fighting serves other roles, e.g., to deter copulation interruptions and rebuff competitors. Our findings support the hypothesis that social systems regulating conflict and promoting females’ choice based on display are fundamental to stable lek evolution. Moreover, our analysis highlights the utility of the REM framework in testing mechanistic hypotheses in behavioral ecology and evolution.

Summary of relational tables in the TSCEvolTree_Aze&2011_CorrJul2018 database

MorphospeciesAze_TableS3

Details for the 339 morphospecies of the Aze & others paper [1], augmented from [1, Appendix S1, Table S3 and Appendix S5, worksheet aM]. The main focus is on clarifying the choice of stratigraphic ranges and ancestry, and incorporating post-publication corrections by the authors of Aze & others or selective corrections/amendments during conversion to TimeScale Creator.

Stratigraphic ranges are given in Ma values; the time scales of the sources for the Ma values are made explicit (via links to table, MorphospeciesAze_TableS3DateRef). Almost all ranges are simple, as per those provided by the 2011 paper, delineated by lowest (start date) and highest occurrence (end date). However, a small number of ranges more closely represent those given by the nominated sources by also including range extensions: “questioned” or “questioned (rare)” for less confident stratigraphic occurrences; and “conjectured”, where a range extension is hypothesized, usually to support an ancestry proposal lacking contiguous stratigraphic occurrences. A proportion (~15 %) of Ma values are corrected where minor differences in Ma values were found between the 2011 paper and the nominated source; however, a systematic check was not conducted across the dataset. A further proportion (~15 %) of Ma values are amended where alternative sources appear to better represent the intention of the 2011 paper; these include a few instances where there would be a conflict with the index (marker) datum sequence of the Wade & others [2] zonation. Corrections to Ma values are accompanied by brief explanatory comments. Minor changes to Ma values were also made by one of us (TA) for a proportion (~17 %) of entries; most of these corresponded to the already invoked corrections or amendments.

Entries for ancestors follow the 2011 paper, with two exceptions in which adjustments to Ma values have removed the overlap in range between ancestor and descendant: a correction made by Tracy Aze (for Pulleniatina finalis, P. obliquiloculata replaced P. spectabilis); and an amendment (for Paragloborotalia pseudokugleri, Dentoglobigerina galavisi is amended to D. globularis). Levels of evidential support for the ancestor–descendant proposals were not critically appraised as part of the TimeScale Creator conversion. However, column [PhylogenyMethod] was employed to distinguish a small number of proposals which were distinctly less (“not well”) or better (“strongly”) supported than the typical “well supported” proposals presumed for this group.

All other information given in [1, Table S3] was incorporated, including indications of morphology, ecology, geography, and analyses made using the Neptune database. This information from Table S3 also included the lists of segments from both morphospecies (ID) and lineage (LID) trees within which each morphospecies occurred; in terms of relational logic, these could be supplanted by a single entry, the code for the lineage containing the highest occurrence of the morphospecies, and this was added manually for the TimeScale Creator conversion.

BiospeciesAze_aL

Details for the 210 lineages of the 2011 paper, augmented from [1, Appendix S5, worksheet aL]. The main focus is to maximize and maintain consistency and transparency between morphospecies and lineages for Ma values of their stratigraphic ranges. This is achieved for the TimeScale Creator conversion by nominating a morphospecies whose Ma value (start or end date) potentially defines the date (start or end) for a lineage; each morphospecies chosen for this is based on the apparent link between morphospecies and lineage dates used in the 2011 paper; this morphospecies is given by column [StartDateOrigLinkMph]. For start dates, ~40 % of lineages could be linked in this way; for end dates, almost all (93 %) were. Where a lineage range point of the 2011 study did not correspond to a morphospecies range point, then this morphospecies is at least used to provide the time scale applied to the date for the lineage.

Entries for ancestral lineages follow the 2011 paper, with two exceptions necessitated by changes in Ma values which place the ancestral lineage outside the date of origin of the descendant lineage: N150-N151-T153, involving the origin of morphospecies Paragloborotalia pseudokugleri; and N52-N54-T53, involving the origin of morphospecies Hirsutella cibaoensis. Levels of evidential support for the ancestor–descendant proposals were not critically appraised as part of the TimeScale Creator conversion. However, column [PhylogenyMethod] was employed to distinguish two proposals that were distinctly less (“not well”) or better (“strongly”) supported than the typical “well supported” proposals presumed for this group. The assignment of branching type as bifurcating or budding in the 2011 paper is incorporated.

Ecogroup and morphogroup allocations follow the 2011 paper (these data were not provided with the 2011 paper, but were indicated by colours employed in [1, Appendices S2, S3]; some colours for lineage morphogroups needed to be corrected; the ecogroup and morphogroup data for lineages were provided for the TimeScale Creator conversion by one of us [TA]). Some minor exceptions to these ecogroup and morphogroups were invoked for the TimeScale Creator conversion, in order to better match those of the contained morphospecies.

MorphospeciesAze_TableS1_Morphogroup

Details for morphogroups used for morphospecies and lineages; as for [1, Appendix 1, Table S1, "Morphogroup"], with explicit colour codes.

MorphospeciesAze_TableS1_Ecogroup

Details for ecogroups used for morphospecies and lineages; as for [1, Appendix 1, Table S1, "Ecogroup"], with explicit colour codes.

MorphospeciesAze_TableS3_EcogroupReference

Sources for ecogroups assigned to morphospecies; as for "Ecogroup reference", taken from [1, Appendix 1, Table S3]; multiple references in the original entries are accorded a row each.

MorphospeciesAze_TableS3_AppendixS1C_References

References for [1, Appendix 1, Table S3 ].

MorphospeciesAze_TableS3DateRef

Sources, and their time-scales, used for Ma values (sources from [1, Appendix 1, Table S3, "Date reference"] "Date reference", Table S3, Appendix 1 of the 2011 paper). The key purpose is to make explicit the time scale against which the source has (apparently) provided the Ma value, essential in order to appropriately recalibrate to the current GTS time scale and also to maintain the capability to recalibrate to future time scales. An important example of this need is where dates from the Paleocene Atlas [3] have here been remeasured directly from the Atlas and so are against the time scale of Berggren & others [4], rather than calibrated to Wade & others [2] as in the 2011 study.

In the interests of transparency and to provide a pointer to recalibration steps needed, a further level of specificity is needed for those sources which imply more than one time scale for Ma values used. For the TimeScale Creator conversion, references to these sources also have the time scale specified. Examples include chapters from the Eocene Atlas [5]. For instance, in order for the TimeScale Creator conversion to record the questionable parts of the stratigraphic ranges given for some Clavigerinella morphospecies by Coxall & Pearson [6], additional start dates for these morphospecies have been measured directly from their Figure 8.1, drawn against the scale of Berggren & Pearson [7]. However, these dates need to be integrated with the Ma values from Coxall & Pearson already used in the 2011 paper, which were presented recalibrated by them to the scale of Wade & others. These two sets of sources are given as, respectively, “Coxall & Pearson (2006: BP05)” (against Berggren & Pearson) and “Coxall & Pearson (2006)” (against the time-scale option of Wade & others which was calibrated to Cande & Kent [8]). Analogous examples came from sources such as Berggren & others, which include some dates for which the usual recalibration is not applicable (reasons are specific to each instance and are indicated in comments fields in table, MorphospeciesAze_TableS3; Appendix S1b includes descriptions of these fields in worksheet, DesignMorphospeciesAze_TableS3, and corresponding data in worksheet, MorphospeciesAze_TableS3).

MorphospeciesAze_TableS3DateRef_DateScale

This simply gives full names for the four time scales requiring recalibration: BKSA95: Berggren & others, 1995 [4] BP05: Berggren & Pearson, 2005 [7] WPBP11(CK95): Wade & others, 2011 [2]; calibrated to Cande & Kent, 1995 [8] WPBP11(GTS04): Wade & others, 2011 [2]; calibrated to Gradstein & others, 2004 (GTS2004) [9].

Wade & others, 2011 Datum

Details for datums relative to zonations, compiled from [2, Tables 1, 3, 4 ].

Zonal (marker) datums are indicated, but other datums are also included, almost all of which provide intrazonal intervals employed for calibration between time scales. Datums specific to the BKSA95 zonation are separately tabulated from those of BP05, allowing calibration between zonations BKSA95, BP05, WPBP11(CK95), and WPBP11(GTS04) (see MorphospeciesAze_TableS3DateRef_DateScale, above). The WPBP11(GTS04) zonation corresponds to GTS2004 and so allows calibration to later GTS time scales (GTS2012, GTS2016).

Additional columns provide brief indications of adjustments needed for calibration, including a small number of alternative datums resulting from revised definitions of zonations. Nomenclatural links are provided for datum-naming taxa.

Global tables:

SpeciesGroupName GenusGroupName ChronosPortal ColoursClofordWebSafeByHue

augmented from TimeScale Creator spreadsheet data:

TimeUnit_ReferenceUnit TimeUnit TSCPlanktonicForaminifersDatum TSCPlanktonicForaminifersDatumMorphospecies

Datapack

CephBase is a dynamic html (dhtml) relational database-driven interactive web site that has been online since 1998. The prototype version of CephBase was developed at Dalhousie Univeristy in Halifax, Canada and was sponsored by the Sloan Foundation following the Workshop on Non-Fish Nekton in Boston, December, 1997. As of 12/2000, CephBase has all the taxa, authorities, and the year the taxa was described online for all of the 703 known living species of cephalopods listed by Sweeney and Roper (1998). CephBase provides taxonomic data, distribution, images, videos, predator and prey data, size, references and scientific contact information for all living species of cephalopods (octopus, squid, cuttlefish and nautilus) in an easy to access, user-friendly manner.

       Information on a particular species can be quickly located by using the search engine; results are listed in table format. Users simply click on a species cephalopod is displayed. Users can also display an alphabetized list of all cephalopod genera. Clicking on a genus leads to a list of all species it contains. For each species, synonymies, type repositories, type localities, references and common names are listed. References are listed in abbreviated form with access to full references. 

       Species Database: 
       Search by scientific, common name or synonym to call up species-specific pages with information such as full taxonomy, type species, names, size, predators, prey, biogeography, distribution maps, country lists, life history, images, videos, references, genetic information links and other internet resources. 

       Image Database: 
       Search our ~1650 cephalopod images which cover all life stages, behaviour, ecology, taxonomy as well as many other aspects of these amazing animals. Each image has a caption, key words, location, photographer and other data. 

       Video Database: 
       There are ~150 video clips in the video database. 

       Reference Database: 
       There are now over 6000 ceph papers in our reference database. 

       Researcher Directory: 
       Looking for a grad school supervisor or cephalopod expert? There are over 400 names in the International Directory of Cephalopod Workers. 

       Predators and Prey: 
       Search by predator, prey or cephalopod species in our predators and prey databases. 

       To answer the question, "Where does it live?", CephBase has 3,175 referenced localities for 328 species served by OBIS.  All latitude and longitude data used to generate maps are from published sources and are listed in tables and referenced. In many cases, the individual specimens used to populate the database can be tracked to a museum repository.

       The purpose of CephBase is to provide taxonomy, life history, distribution, fisheries, and ecology for all living cephalopod species (i.e., octopus, squid, cuttlefish and nautilus). Such a global database will facilitate collaboration both within the cephalopod community and among all marine sciences.

       The data can be accessed through the following web portals (see Related URL field below):
       -OBIS, Ocean Biogeographic Information System, CoML (Census of Marine Life) web portal.
       -EurOBIS, the European Ocean Biogeographique Information System. 
       -SCAR-MarBIN, the Marine Biodiversity Information Network, Scientific Committee on Antarctic Research, International Council for Science.

This is a mixed-methods data collection. The study is part of the Rural Economy and Land Use (RELU) programme.

The Governance of Livestock Disease (GoLD) project ran from November 2007 to November 2010. The overall aim of the project was to develop an interdisciplinary framework to elucidate the governance of livestock diseases (i.e. the reciprocal impacts of dynamic changes to epidemiology, policy, law and economy) in order to better inform stakeholders of the potential impact of different policy and regulatory changes. Two kinds of data (referred to as 'datasets' below, some of which had been collected under earlier grants) were used to complete this work and both are available from the UK Data Archive within this study:

• Dataset 1: questionnaire data were collected from 148 farmers and serum samples were collected from all cattle in a subset of 114 farms. Data collection was funded by the Department for the Environment, Food and Rural Affairs (DEFRA) project SE3026, Bovine TB Transmission in Restocked Herds: Risk Factors and Dynamics, conducted between June 2002 and March 2006. The serum samples were subsequently analysed for antibodies to five endemic diseases in the Biotechnology and Biological Sciences Research Council (BBSRC) project BBS/B/04854 Epidemiology and Transmission Dynamics of Endemic Infectious Disease in the British Cattle Population, conducted between October 2004 and February 2008. The relational database includes both the questionnaire data and the quantitative serological data.
• Dataset 2: within the Economic and Social Research Council (ESRC) RELU funded grant Decision-making Frameworks in Management of Livestock disease: Interaction of Epidemiology, Economics and Politics, which ran from November 2007 to November 2010, the project team conducted semi-structured interviews with 30 farmers concentrating on their attitudes to endemic disease, information sources and relationship with their veterinarian.

The farmer interviews covered: background and details about farm; general cattle disease on the farm; six specific cattle diseases: bovine viral diarrhoea virus (BVD), Infectious Bovine Rhinotracheitis (IBR), bovine tuberculosis (TB), Leptospira, Neospora and Johnes disease; control of disease; cattle in and out of the herd; neighbouring farms; finance, cattle disease governance; whether respondent thinks future disease situation in cattle in the wider industry will get better or worse; other important factors in cattle disease management.

The relational database CSV output table files include results from two questionnaires that covered 148 farms; the first questionnaire has approximately 12 sections, with 10 to 50 quantitative questions per section; the second questionnaire has 2 sections, with a similar number of questions. Serum samples were taken three times from farms; all adult animals (>2yrs old) were sampled. Each sample was tested for five different diseases by ELISA test, and antigen for one infection. The SQL schema files define the database structure. Further information on the database structure and table relationships is included in the database documentation.

Further information for this study may be found through the ESRC Research Catalogue webpage: The Governance of Livestock Disease webpage.

The data set comprises hydrographic, biogeochemical and biological data, including measurements of temperature, salinity and attenuance, plus concentrations of parameters such as nutrients, pigments, urea, hydrocarbons, sedimentation flux, sulphur and dissolved carbon. Analyses of bacterial, zooplankton and phytoplankton communities were also undertaken. The oceanographic data were supplemented by measurements of surface meteorological parameters. Data were collected across three repeated sections: one along the Gulf of Oman; a section at 67deg East from 8 to 14.5deg North; and a major section from 8deg North, 67 deg East to the coast of Oman. Other one-off sections were also traversed in the Arabian Sea and Gulf of Oman areas. Measurements were collected during two cruises: one between 27 August and the 4 October 1994 and the other between the 16 November and the 19 December 1994. Sections were covered by underway surface ocean measurements (one minute sampling of multiple parameters providing some 5 million measurements) complemented by a total of 21 CTD/water-bottle stations, 14 of which were repeated. ARABESQUE was organised by the Plymouth Marine Laboratory of NERC's Centre for Coastal and Marine Sciences and involved the University of Wales, Bangor; Queen's University of Belfast; University of East Anglia; University of Edinburgh; University of Newcastle; the Bedford Institute of Oceanography, Canada; the Max Planck Institute for Limnology, Germany and the Sultan Qaboos University, Oman. Data management support for the project was provided by the British Oceanographic Data Centre. All data collected as part of the project were lodged with BODC who had responsibility for assembling, calibrating, quality controlling and fully documenting the data. BODC checked for instrument spikes or malfunction, values beyond the calibration range, unreasonable ratios of chemical constituents and unreasonable deviations from climatological means. Data were assembled into a relational database, complete with supporting documentation and a user manual. The full data set has been published by BODC on CD-ROM complete with user interface.

Timescale Creator–database customization

Features provided by Timescale Creator enhance the information which can be gleaned from the 2011 trees. These features can be provided either from functions already built into Timescale Creator, or via “in-house” programming within the database which has exploited the built-in functions to provide data and information on key issues of interest to the case study. It is this flexibility provided by the combination of Timescale Creator functions and datapacks programmed from the back-end relational database which is showcased below.

Groups

Colours were used in the original 2011 trees [1, Appendices 2, 3 ], and now in the Timescale Creator trees, to display eco- and morpho-groups (respectively). The Timescale Creator trees also add coloured group labels (rather than colouring the range labels as in the original trees), and this allows identification of groups without recourse to the legend. These group labels are positioned on ancestor–descendant branches, but have here been programmed to display only when the group membership changes from ancestor to descendant. As a result, they have the added advantage of highlighting origins and reappearances of the selected groups or properties in a phylogenetic context. A handy use of this feature is when, for example, this is programmed to apply to the generic assignment of morphospecies, making polyphyletic morphogenera, intentioned or otherwise, easy to spot.

Lineage labels

To label range lines on the lineage tree, the Timescale Creator version has been programmed to augment each lineage code with its list of contained morphospecies, e.g., the listing appended to Lineage N1-N3 is “H. holmdelensis > G. archeocompressa > G. planocompressa > G. compressa“. The morphospecies series in these listings is ordered by lowest occurrence, and so the >’s denote stratigraphic succession. (The >’s do not necessarily represent ancestor–descendant relationships; of course only a single line of descent could be expressed in such a format.) This allows the lineage and its proposed morphological succession to be grasped much more easily, including a ready comparison with the morphospecies tree.

Pop-ups

Pop-ups provide the most ample opportunity within Timescale Creator to provide access to supporting information for trees. Because pop-up windows are flexibly resizable and are coded in html, textual content has in effect few quota limitations and, in fact, can be employed to view external sources such as Internet sites and image files without the need to store them in the pop-up itself. They can also be programmed to follow a format tailored for the subject matter, as is done here.

Pop-ups for the morphospecies tree display the contents of the 2011 paper’s summary table [1, Appendix S1, Table S3], including decoding of eco- and morpho-group numbers, range statistics from the Neptune portal, and tailoring the reference list to each morphospecies. They also incorporate the ancestor [from 1, Appendix S5, worksheet aM], specify the type of cladogenetic event (all are, in fact, budding for this budding/bifurcating topology [2]), and level of support for the ancestor–descendant proposal (see § Branches). Lineages containing the morphospecies are listed, along with their morphospecies content and age range (for details, see § Linkages between morphospecies and lineage trees [3]). Also included are the binomen’s original assignation and, where available, links to portals, Chronos [4][5-7] and the World Register of Marine Species (WoRMS) [8].

Range lines

Range-line styles have been used for the Timescale Creator version of the 2011 trees to depict four levels of confidence for ranges. Apart from accepted ranges (lines of usual thickness), two less-confident records of stratigraphic occurrence are depicted: “questioned” (thin line) and “questioned-and-rare” (broken line). For extensions to ranges that are not based on stratigraphic occurrences but are hypothesized (for various reasons), a “conjectured” range is separately recognised (dotted line) to ensure that stratigraphic and hypothesized categories are not conflated. There is an option to attach age labels (in Ma) to range lines, providing the chart with an explicit deep-time positioning throughout.

Branches

Similarly to ranges, branch-line styles have been used to depict three levels of stratophenetic support for ancestry. Almost all ancestor–descendant proposals for the 2011 study are presumed to be “Well Supported” (correspondence between detailed stratigraphic sequences and plausible phyletic series; drawn as a broken line). A small number have been categorised as less or better supported than the usual: “Not Well Supported” (only broad correspondence between stratigraphic order and suggestive phyletic series; drawn as a dotted line); or “Strongly Supported” (detailed morphometric–stratigraphic sequences from ancestor to descendant; continuous line).

Linkages between morphospecies and lineage trees

Many range points of the lineages of the 2011 study are herein directly linked to those of included morphospecies: not quite half of start dates and almost all of end dates. Brief details of this linkage are displayed in the “Stratigraphic Range (continued)” section of the pop-up, where the linkage will usually result in the same precalibrated Ma value between lineage and morphospecies range points, but these values will differ where there has been a correction or amendment of the original Ma value. The reason for choosing the morphospecies range point is usually briefly indicated. Where the original Ma value of the lineage range point is retained and not directly linked to a morphospecies point, the morphospecies and its time scale that are employed nonetheless for calibration are indicated.

Pop-ups are also employed to more easily appreciate the linkages between morphospecies and lineages, following from the morphospecies content of lineages. These are displayed both in terms of the lineages in which a morphospecies occurs and in terms of the morphospecies included in a lineage, along with other information to help track these interrelationships.

1. Aze T, Ezard TH, Purvis A, Coxall HK, Stewart DR, Wade BS, et al. A phylogeny of Cenozoic macroperforate planktonic foraminifera from fossil data. Biological Reviews of the Cambridge Philosophical Society. 2011;86(4):900-27. doi: 10.1111/j.1469-185X.2011.00178.x.
2. see § Data, topologies, and taxa of the 2011 study’s trees: Tree topologies, above
3. a morphospecies contained in more than one lineage is depicted in Figure 20a
4. Support for on-going activity on the foraminiferal section of Chronos [116] no longer appears viable; other portals may need to be linked in later versions e.g., pforams@mikrotax [117, 118]
5. Huber BT. Foraminiferal databases (Mesozoic Paleocene, Eocene Planktonic Foraminifera Taxonomic databases), Chronos Portal Washington (DC, USA): Consortium for Ocean Leadership for the Chronos Internal Coordinating Committee (Iowa State University and the National Science Foundation). Available from: http://portal.chronos.org/gridsphere/gridsphere?cid=foram_working_group (not updated in recent years).
6. Young J, Huber BT, Bown P, Wade BS. pforams@mikrotax (UK Natural Environment Research Council), within mikrotax.org London: University College London. Available from: http://www.mikrotax.org/pforams/index.html.
7. Huber BT, Petrizzo MR, Young JR, Falzoni F, Gilardoni SE, Bown PR, et al. Pforams@microtax: a new online taxonomic database for planktonic foraminifera. Micropaleontology. 2017;62(6):429-38.
8. Hayward BW, Le Coze F, Gross O. World Foraminifera Database, World Register of Marine Species (WoRMS) Vlaams Instituut voor de Zee (Flanders Marine Institute), Oostende (Belgium): WoRMS Editorial Board; 2018 [2018-01-09]. Available from: http://www.marinespecies.org/foraminifera, http://www.marinespecies.org doi:10.14284/170

This data set was centralized for the Marine Gap Analysis Project of the Hawaii Natural Heritage Program. It was obtained from various principle investigators for a multitude of projects. It includes surveys from 183 locations on the eight main Hawaiian Islands. The data were placed in a relational database.

The dataset contains physical, biological and chemical oceanographic measurements, and meteorological data. Hydrographic measurements include temperature, salinity, current velocities, attenuance, dissolved oxygen and fluorescence, while water samples were analysed for concentrations of nutrients, pigments, suspended particulates, metals and halocarbons. Samples were also collected for phytoplankton and zooplankton analyses, while results from production experiments are also included in the data set. These oceanographic data are supplemented by surface meteorological measurements. The data were collected at 357 sites in the NE Atlantic, 308 of which are from cruises centering on 20 W, 47 to 60 N, 16 from the Cape Verde Islands and 33 in a coccolithophore bloom just south of Iceland. Measurements were taken from 3 cruises in 1989, 6 cruises in 1990 and 2 cruises in 1991. The data were collected via (i) underway sampling (SeaSoar Undulating Oceanographic Recorder (UOR), hull-mounted acoustic Doppler current profiler (ADCP), meteorology and surface ocean parameters) of which there are 793430 records at 30 second intervals from 11 cruises and (ii) discrete sampling (conductivity-temperature-depth (CTD) and expendable bathythermograph (XBT) casts, bottle stations, net hauls, productivity incubations, stand alone pump (SAP) and sediment trap deployments, cores) of which there are 2215 deployments/experiments. The aim of the Biogeochemical Ocean Flux Study (BOFS) Community Research Project was to study the role of oceans in the global cycling of carbon. The data were collected and supplied by UK participants in the Joint Global Ocean Flux Study (JGOFS). The British Oceanographic Data Centre (BODC) had responsibility for calibrating, processing, quality controlling and documenting the data and assembling the final data set. The underway data are stored as time series for each cruise merged with the navigation data. The data are fully quality controlled. Checks were made for instrument malfunction, fouling, constant values, spikes, spurious values, calibration errors and baseline corrections. The discrete data are stored in a relational database (Oracle RDBMS), mainly as vertical profiles and are uniquely identified by a combination of deployment number and depth.

In response to declines in reef fishes, the Hawaii state legislature created the West Hawaii Regional Fishery Management Area in 1998 to improve fishery resources (Act 306). The West Hawaii Aquarium Project (WHAP) was funded by the Hawaii Coral Reef Initiative to monitor to fish populations and quantify the habitats in this region. This dataset consists of an MS Access relational database of all monitoring data from 1999-2003. The relational database of this dataset includes some of the data held in NODC Accession 0000938, however, it would be best to examine each accession carefully. The relational database of this accession has fewer tables and less parameters.

During initial funding under CRAMP in 1998-99, 23 permanent study sites were established positioned in all of the proposed Fish Replenishment Areas (FRAs) as well as eight sites where fish collecting is know to occur ("impact"), and six managed areas where aquarium fish collection is prohibited (three Marine Life Conservation Districts (MLCDs) and three FMAs or "control"). Initial surveys confirm that aquarium fish collecting impacts are significant but vary along the coastline.

Abstract copyright UK Data Service and data collection copyright owner.

This is a mixed-methods data collection. The study is part of the Rural Economy and Land Use (RELU) programme.

The Governance of Livestock Disease (GoLD) project ran from November 2007 to November 2010. The overall aim of the project was to develop an interdisciplinary framework to elucidate the governance of livestock diseases (i.e. the reciprocal impacts of dynamic changes to epidemiology, policy, law and economy) in order to better inform stakeholders of the potential impact of different policy and regulatory changes. Two kinds of data (referred to as 'datasets' below, some of which had been collected under earlier grants) were used to complete this work and both are available from the UK Data Archive within this study:

• Dataset 1: questionnaire data were collected from 148 farmers and serum samples were collected from all cattle in a subset of 114 farms. Data collection was funded by the Department for the Environment, Food and Rural Affairs (DEFRA) project SE3026, Bovine TB Transmission in Restocked Herds: Risk Factors and Dynamics, conducted between June 2002 and March 2006. The serum samples were subsequently analysed for antibodies to five endemic diseases in the Biotechnology and Biological Sciences Research Council (BBSRC) project BBS/B/04854 Epidemiology and Transmission Dynamics of Endemic Infectious Disease in the British Cattle Population, conducted between October 2004 and February 2008. The relational database includes both the questionnaire data and the quantitative serological data.
• Dataset 2: within the Economic and Social Research Council (ESRC) RELU funded grant Decision-making Frameworks in Management of Livestock disease: Interaction of Epidemiology, Economics and Politics, which ran from November 2007 to November 2010, the project team conducted semi-structured interviews with 30 farmers concentrating on their attitudes to endemic disease, information sources and relationship with their veterinarian.

The farmer interviews covered: background and details about farm; general cattle disease on the farm; six specific cattle diseases: bovine viral diarrhoea virus (BVD), Infectious Bovine Rhinotracheitis (IBR), bovine tuberculosis (TB), Leptospira, Neospora and Johnes disease; control of disease; cattle in and out of the herd; neighbouring farms; finance, cattle disease governance; whether respondent thinks future disease situation in cattle in the wider industry will get better or worse; other important factors in cattle disease management.

The relational database CSV output table files include results from two questionnaires that covered 148 farms; the first questionnaire has approximately 12 sections, with 10 to 50 quantitative questions per section; the second questionnaire has 2 sections, with a similar number of questions. Serum samples were taken three times from farms; all adult animals (>2yrs old) were sampled. Each sample was tested for five different diseases by ELISA test, and antigen for one infection. The SQL schema files define the database structure. Further information on the database structure and table relationships is included in the database documentation.

Further information for this study may be found through the ESRC Research Catalogue webpage: The Governance of Livestock Disease webpage.

Main Topics:

Governance of cattle and other livestock disease; serology; livestock management.

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