Dataset Search Results

This repository includes scripts and datasets for the paper, "TreeMerge: A new method for improving the scalability of species tree estimation methods." The latest version of TreeMerge can be downloaded from Github (https://github.com/ekmolloy/treemerge).

Data and documentation for Ornithological Applications manuscript “Integrating multiple data sources improves prediction and inference for upland game bird occupancy models” by Robert L. Emmet, Thomas J. Benson, Maximilian L. Allen, and Kirk W. Stodola We combined data from the North American Breeding Bird Survey and eBird with a targeted survey (IDNR upland game) to estimate habitat use of northern bobwhite and ring-necked pheasant in Illinois and to document the efficiency and overlap among the various data sources. Data include, eBird, USGS Breeding Bird Survey, National Land Cover Database, Upland game bird surveys, stream data)

Data sets from "DISCO+QR: Rooting Species Trees in the Presence of GDL and ILS." It contains trees and sequences simulated with gene duplication and loss under a variety of different conditions. Note: - trees.tar.gz contains the simulated gene-family trees used in our experiments (both true trees from SimPhy as well as trees estimated from alignments). - alignments.tar.gz contains simulated sequence data used for estimating the gene-family trees

This is a simulated sequence dataset generated using INDELible and processed via a sequence fragmentation procedure.

This dataset contains RNASim1000, Cox1-Het datasets as well as analyses of RNASim1000, Cox1-Het, and 1000M1(HF).

The dataset contains a complete example (inputs, outputs, codes, intermediate results, visualization webpage) of executing Height Above Nearest Drainage HAND workflow with CyberGIS-Jupyter.

This dataset provides the raw data, code and related figures for the paper, "Anomalous Spin-Orbit Torques in Magnetic Single-Layer Films."

Dataset associated with "Hiding in plain sight: genetic confirmation of putative Louisiana Fatmucket Lampsilis hydiana in Illinois" as submitted to Freshwater Mollusk Biology and Conservation by Stodola et al. Images are from cataloged specimens from the Illinois Natural History Survey (INHS) Mollusk Collection in Champaign, Illinois that were used for genetic research. File names indicate the species as confirmed in Stodola et al. (i.e., Lampsilis siliquoidea or Lampsilis hydiana) followed by the INHS Mollusk Collection catalog number, followed by the individual specimen number, followed by shell view (interior or exterior). If no specimen number is noted in the file name, there is only one specimen for that catalog number. For example: Lsiliquoidea_46515_1_2_3_exterior. Images were created by photographing specimens on a metric grid in an OrTech Photo-e-Box Plus with a Nikon D610 single lens reflex camera using a 60mm lens. Post-processing of images (cropping, image rotation, and auto contrast) occurred in Adobe Photoshop and saved as TIFF files using no image compression, interleaved pixel order, and IBM PC Byte Order. One additional partial lot, INHS Mollusk Catalog No. 37059 (shown with both interior and exterior view in one image), is included for reference but was not genetically sequenced. A .csv file contains an index of all specimens photographed. SPECIES: species confirmed using genetic analyses GENE: cox1 or nad1 mitochondrial gene ACCESSION: GenBank accession number INHS CATALOG NO: Illinois Natural History Survey Mollusk Collection Catalog number WATERBODY: waterbody where specimen was collected PUTATIVE SPECIES: species determination based on morphological characters prior to genetic analysis Phylogenetic sequence data (.nex files) were aligned using BioEdit (Hall, T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41:95-98.). Pertinent methodology for the analysis are contained within the manuscript submittal for Stodola et al. to Freshwater Mollusk Biology and Conservation. In these files, "N" is a standard symbol for an unknown base.

Author-ity 2009 baseline dataset. Prepared by Vetle Torvik 2009-12-03 The dataset comes in the form of 18 compressed (.gz) linux text files named authority2009.part00.gz - authority2009.part17.gz. The total size should be ~17.4GB uncompressed. &bull; How was the dataset created? The dataset is based on a snapshot of PubMed (which includes Medline and PubMed-not-Medline records) taken in July 2009. A total of 19,011,985 Article records and 61,658,514 author name instances. Each instance of an author name is uniquely represented by the PMID and the position on the paper (e.g., 10786286_3 is the third author name on PMID 10786286). Thus, each cluster is represented by a collection of author name instances. The instances were first grouped into "blocks" by last name and first name initial (including some close variants), and then each block was separately subjected to clustering. Details are described in <i>Torvik, V., & Smalheiser, N. (2009). Author name disambiguation in MEDLINE. ACM Transactions On Knowledge Discovery From Data, 3(3), doi:10.1145/1552303.1552304</i> <i>Torvik, V. I., Weeber, M., Swanson, D. R., & Smalheiser, N. R. (2005). A Probabilistic Similarity Metric for Medline Records: A Model for Author Name Disambiguation. Journal Of The American Society For Information Science & Technology, 56(2), 140-158. doi:10.1002/asi.20105</i> Note that for Author-ity 2009, some new predictive features (e.g., grants, citations matches, temporal, affiliation phrases) and a post-processing merging procedure were applied (to capture name variants not capture during blocking e.g. matches for subsets of compound last name matches, and nicknames with different first initial like Bill and William), and a temporal feature was used -- this has not yet been written up for publication. &bull; How accurate is the 2009 dataset (compared to 2006 and 2009)? The recall reported for 2006 of 98.8% has been much improved in 2009 (because common last name variants are now captured). Compared to 2006, both years 2008 and 2009 overall seem to exhibit a higher rate of splitting errors but lower rate of lumping errors. This reflects an overall decrease in prior probabilites -- possibly because e.g. a) new prior estimation procedure that avoid wild estimates (by dampening the magnitude of iterative changes); b) 2008 and 2009 included items in Pubmed-not-Medline (including in-process items); and c) and the dramatic (exponential) increase in frequencies of some names (J. Lee went from ~16,000 occurrences in 2006 to 26,000 in 2009.) Although, splitting is reduced in 2009 for some special cases like NIH funded investigators who list their grant number of their papers. Compared to 2008, splitting errors were reduced overall in 2009 while maintaining the same level of lumping errors. &bull; What is the format of the dataset? The cluster summaries for 2009 are much more extenstive than the 2008 dataset. Each line corresponds to a predicted author-individual represented by cluster of author name instances and a summary of all the corresponding papers and author name variants (and if there are > 10 papers in the cluster, an identical summary of the 10 most recent papers). Each cluster has a unique Author ID (which is uniquely identified by the PMID of the earliest paper in the cluster and the author name position. The summary has the following tab-delimited fields: 1. blocks separated by '||'; each block may consist of multiple lastname-first initial variants separated by '|' 2. prior probabilities of the respective blocks separated by '|' 3. Cluster number relative to the block ordered by cluster size (some are listed as 'CLUSTER X' when they were derived from multiple blocks) 4. Author ID (or cluster ID) e.g., bass_c_9731334_2 represents a cluster where 9731334_2 is the earliest author name instance. Although not needed for uniqueness, the id also has the most frequent lastname_firstinitial (lowercased). 5. cluster size (number of author name instances on papers) 6. name variants separated by '|' with counts in parenthesis. Each variant of the format lastname_firstname middleinitial, suffix 7. last name variants separated by '|' 8. first name variants separated by '|' 9. middle initial variants separated by '|' ('-' if none) 10. suffix variants separated by '|' ('-' if none) 11. email addresses separated by '|' ('-' if none) 12. range of years (e.g., 1997-2009) 13. Top 20 most frequent affiliation words (after stoplisting and tokenizing; some phrases are also made) with counts in parenthesis; separated by '|'; ('-' if none) 14. Top 20 most frequent MeSH (after stoplisting; "-") with counts in parenthesis; separated by '|'; ('-' if none) 15. Journals with counts in parenthesis (separated by "|"), 16. Top 20 most frequent title words (after stoplisting and tokenizing) with counts in parenthesis; separated by '|'; ('-' if none) 17. Co-author names (lowercased lastname and first/middle initials) with counts in parenthesis; separated by '|'; ('-' if none) 18. Co-author IDs with counts in parenthesis; separated by '|'; ('-' if none) 19. Author name instances (PMID_auno separated '|') 20. Grant IDs (after normalization; "-" if none given; separated by "|"), 21. Total number of times cited. (Citations are based on references extracted from PMC). 22. h-index 23. Citation counts (e.g., for h-index): PMIDs by the author that have been cited (with total citation counts in parenthesis); separated by "|" 24. Cited: PMIDs that the author cited (with counts in parenthesis) separated by "|" 25. Cited-by: PMIDs that cited the author (with counts in parenthesis) separated by "|" 26-47. same summary as for 4-25 except that the 10 most recent papers were used (based on year; so if paper 10, 11, 12... have the same year, one is selected arbitrarily)

This dataset contains raw data associated with the red fox Y-chromosome assembly (see https://doi.org/10.3390/genes10060409). It includes a fasta file of the 171 scaffolds from the red fox reference genome assembly identified as likely to contain Y-chromosome sequence, the raw BLAST results, and the ABySS assemblies described in the manuscript.

Self-citation analysis data based on PubMed Central subset (2002-2005) ---------------------------------------------------------------------- Created by Shubhanshu Mishra, Brent D. Fegley, Jana Diesner, and Vetle Torvik on April 5th, 2018 ## Introduction This is a dataset created as part of the publication titled: Mishra S, Fegley BD, Diesner J, Torvik VI (2018) Self-Citation is the Hallmark of Productive Authors, of Any Gender. PLOS ONE. It contains files for running the self citation analysis on articles published in PubMed Central between 2002 and 2005, collected in 2015. The dataset is distributed in the form of the following tab separated text files: * Training_data_2002_2005_pmc_pair_First.txt (1.2G) - Data for first authors * Training_data_2002_2005_pmc_pair_Last.txt (1.2G) - Data for last authors * Training_data_2002_2005_pmc_pair_Middle_2nd.txt (964M) - Data for middle 2nd authors * Training_data_2002_2005_pmc_pair_txt.header.txt - Header for the data * COLUMNS_DESC.txt file - Descriptions of all columns * model_text_files.tar.gz - Text files containing model coefficients and scores for model selection. * results_all_model.tar.gz - Model coefficient and result files in numpy format used for plotting purposes. v4.reviewer contains models for analysis done after reviewer comments. * README.txt file ## Dataset creation Our experiments relied on data from multiple sources including properitery data from [Thompson Rueter's (now Clarivate Analytics) Web of Science collection of MEDLINE citations](<a href="https://clarivate.com/products/web-of-science/databases/">https://clarivate.com/products/web-of-science/databases/</a>). Author's interested in reproducing our experiments should personally request from Clarivate Analytics for this data. However, we do make a similar but open dataset based on citations from PubMed Central which can be utilized to get similar results to those reported in our analysis. Furthermore, we have also freely shared our datasets which can be used along with the citation datasets from Clarivate Analytics, to re-create the datased used in our experiments. These datasets are listed below. If you wish to use any of those datasets please make sure you cite both the dataset as well as the paper introducing the dataset. * MEDLINE 2015 baseline: <a href="https://www.nlm.nih.gov/bsd/licensee/2015_stats/baseline_doc.html">https://www.nlm.nih.gov/bsd/licensee/2015_stats/baseline_doc.html</a> * Citation data from PubMed Central (original paper includes additional citations from Web of Science) * Author-ity 2009 dataset: - Dataset citation: <a href="https://doi.org/10.13012/B2IDB-4222651_V1">Torvik, Vetle I.; Smalheiser, Neil R. (2018): Author-ity 2009 - PubMed author name disambiguated dataset. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4222651_V1</a> - Paper citation: <a href="https://doi.org/10.1145/1552303.1552304">Torvik, V. I., & Smalheiser, N. R. (2009). Author name disambiguation in MEDLINE. ACM Transactions on Knowledge Discovery from Data, 3(3), 1–29. https://doi.org/10.1145/1552303.1552304</a> - Paper citation: <a href="https://doi.org/10.1002/asi.20105">Torvik, V. I., Weeber, M., Swanson, D. R., & Smalheiser, N. R. (2004). A probabilistic similarity metric for Medline records: A model for author name disambiguation. Journal of the American Society for Information Science and Technology, 56(2), 140–158. https://doi.org/10.1002/asi.20105</a> * Genni 2.0 + Ethnea for identifying author gender and ethnicity: - Dataset citation: <a href="https://doi.org/10.13012/B2IDB-9087546_V1">Torvik, Vetle (2018): Genni + Ethnea for the Author-ity 2009 dataset. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9087546_V1</a> - Paper citation: <a href="https://doi.org/10.1145/2467696.2467720">Smith, B. N., Singh, M., & Torvik, V. I. (2013). A search engine approach to estimating temporal changes in gender orientation of first names. In Proceedings of the 13th ACM/IEEE-CS joint conference on Digital libraries - JCDL ’13. ACM Press. https://doi.org/10.1145/2467696.2467720</a> - Paper citation: <a href="http://hdl.handle.net/2142/88927">Torvik VI, Agarwal S. Ethnea -- an instance-based ethnicity classifier based on geo-coded author names in a large-scale bibliographic database. International Symposium on Science of Science March 22-23, 2016 - Library of Congress, Washington DC, USA. http://hdl.handle.net/2142/88927</a> * MapAffil for identifying article country of affiliation: - Dataset citation: <a href="https://doi.org/10.13012/B2IDB-4354331_V1">Torvik, Vetle I. (2018): MapAffil 2016 dataset -- PubMed author affiliations mapped to cities and their geocodes worldwide. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4354331_V1</a> - Paper citation: <a href="http://doi.org/10.1045/november2015-torvik">Torvik VI. MapAffil: A Bibliographic Tool for Mapping Author Affiliation Strings to Cities and Their Geocodes Worldwide. D-Lib magazine : the magazine of the Digital Library Forum. 2015;21(11-12):10.1045/november2015-torvik</a> * IMPLICIT journal similarity: - Dataset citation: <a href="https://doi.org/10.13012/B2IDB-4742014_V1">Torvik, Vetle (2018): Author-implicit journal, MeSH, title-word, and affiliation-word pairs based on Author-ity 2009. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4742014_V1</a> * Novelty dataset for identify article level novelty: - Dataset citation: <a href="https://doi.org/10.13012/B2IDB-5060298_V1">Mishra, Shubhanshu; Torvik, Vetle I. (2018): Conceptual novelty scores for PubMed articles. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5060298_V1</a> - Paper citation: <a href="https://doi.org/10.1045/september2016-mishra"> Mishra S, Torvik VI. Quantifying Conceptual Novelty in the Biomedical Literature. D-Lib magazine : The Magazine of the Digital Library Forum. 2016;22(9-10):10.1045/september2016-mishra</a> - Code: <a href="https://github.com/napsternxg/Novelty">https://github.com/napsternxg/Novelty</a> * Expertise dataset for identifying author expertise on articles: * Source code provided at: <a href="https://github.com/napsternxg/PubMed_SelfCitationAnalysis">https://github.com/napsternxg/PubMed_SelfCitationAnalysis</a> **Note: The dataset is based on a snapshot of PubMed (which includes Medline and PubMed-not-Medline records) taken in the first week of October, 2016.** Check <a href="https://www.nlm.nih.gov/databases/download/pubmed_medline.html">here</a> for information to get PubMed/MEDLINE, and NLMs data Terms and Conditions Additional data related updates can be found at <a href="http://abel.ischool.illinois.edu">Torvik Research Group</a> ## Acknowledgments This work was made possible in part with funding to VIT from <a href="https://projectreporter.nih.gov/project_info_description.cfm?aid=8475017&icde=18058490">NIH grant P01AG039347</a> and <a href="http://www.nsf.gov/awardsearch/showAward?AWD_ID=1348742">NSF grant 1348742</a>. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ## License Self-citation analysis data based on PubMed Central subset (2002-2005) by Shubhanshu Mishra, Brent D. Fegley, Jana Diesner, and Vetle Torvik is licensed under a Creative Commons Attribution 4.0 International License. Permissions beyond the scope of this license may be available at <a href="https://github.com/napsternxg/PubMed_SelfCitationAnalysis">https://github.com/napsternxg/PubMed_SelfCitationAnalysis</a>.

Transport and MFM data of brickwork artificial spin ice composed of permalloy are included, which are reproductions of the data in an article named "Magnetic response of brickwork artificial spin ice". Transport data represent magnetic response of connected brickwork artificial spin ice, and MFM data represent how both connected and disconnected brickwork artificial spin ice react to external magnetic fields. SEM images of typical samples are included, where individual nanowire leg (island) is approximately 660 nm long and 140 nm wide with a 40 nm thickness. For the transport, each sample was measured in a longitudinal and a transverse geometry. Red curves are the 2500 Oe to -2500 Oe sweeps and the blue curves are -2500 Oe to 2500 Oe sweeps. Transport measurements were taken by using a standard 4-wire technique. Each plot was saved in pdf format.

This page contains the data for the publication "Regulation of growth and cell fate during tissue regeneration by the two SWI/SNF chromatin-remodeling complexes of Drosophila" published in Genetics, 2020

This data set includes all of data related to strain-resilient FETs based on 2D heterostructures including optical images of FETs, Raman characteristics data, Transport measurement data, and AFM topography data.

Wikipedia category tree embeddings based on wikipedia SQL dump dated 2017-09-20 (<a href="https://archive.org/download/enwiki-20170920">https://archive.org/download/enwiki-20170920</a>) created using the following algorithms: * Node2vec * Poincare embedding * Elmo model on the category title The following files are present: * wiki_cat_elmo.txt.gz (15G) - Elmo embeddings. Format: category_name (space replaced with "_") <tab> 300 dim space separated embedding. * wiki_cat_elmo.txt.w2v.gz (15G) - Elmo embeddings. Format: word2vec format can be loaded using Gensin Word2VecKeyedVector.load_word2vec_format. * elmo_keyedvectors.tar.gz - Gensim Word2VecKeyedVector format of Elmo embeddings. Nodes are indexed using * node2vec.tar.gz (3.4G) - Gensim word2vec model which has node2vec embedding for each category identified using the position (starting from 0) in category.txt * poincare.tar.gz (1.8G) - Gensim poincare embedding model which has poincare embedding for each category identified using the position (starting from 0) in category.txt * wiki_category_random_walks.txt.gz (1.5G) - Random walks generated by node2vec algorithm (https://github.com/aditya-grover/node2vec/tree/master/node2vec_spark), each category identified using the position (starting from 0) in category.txt * categories.txt - One category name per line (with spaces). The line number (starting from 0) is used as category ID in many other files. * category_edges.txt - Category edges based on category names (with spaces). Format from_category <tab> to_category * category_edges_ids.txt - Category edges based on category ids, each category identified using the position (starting from 1) in category.txt * wiki_cats-G.json - NetworkX format of category graph, each category identified using the position (starting from 1) in category.txt Software used: * <a href="https://github.com/napsternxg/WikiUtils">https://github.com/napsternxg/WikiUtils</a> - Processing sql dumps * <a href="https://github.com/napsternxg/node2vec">https://github.com/napsternxg/node2vec</a> - Generate random walks for node2vec * <a href="https://github.com/RaRe-Technologies/gensim">https://github.com/RaRe-Technologies/gensim</a> (version 3.4.0) - generating node2vec embeddings from random walks generated usinde node2vec algorithm * <a href="https://github.com/allenai/allennlp">https://github.com/allenai/allennlp</a> (version 0.8.2) - Generate elmo embeddings for each category title Code used: * wiki_cat_node2vec_commands.sh - Commands used to * wiki_cat_generate_elmo_embeddings.py - generate elmo embeddings * wiki_cat_poincare_embedding.py - generate poincare embeddings

This dataset includes early embryogenesis and post-embryonic development of Soybean cyst nematode.

Mist netting data for little brown bats (Myotis lucifugus) in McHenry County, Illinois and output of acoustic data processed using Kaleidoscope (Version 5.1.9, Bats of North America 5.1.0; Wildlife Acoustics) auto-identification software. Associated survey metadata and landcover metrics calculated using Fragstats included.

This is a sample 5 minute video of an E coli bacterium swimming in a microfluidic chamber as well as some supplementary code files to be used with the Matlab code available at https://github.com/dfraebel/CellTracking

The text file contains the original aligned DNA nucleotide sequence data used in the phylogenetic analyses of Feng et al. (in review), comprising the 3 protein-coding genes (histone H3, cytochrome oxidase I and 2) and 2 ribosomal genes (28S D8 and 16S). The text file is marked up according to the standard NEXUS format commonly used by various phylogenetic analysis software packages. The file will be parsed automatically by a variety of programs that recognize NEXUS as a standard bioinformatics file format. The first six lines of the file identify the file as NEXUS, indicate that the file contains data for 257 taxa (species) and 2995 characters (nucleotide positions), indicate that the characters are DNA sequence, that gaps inserted into the DNA sequence alignment are indicated by a dash, and that missing data are indicated by a question mark. The remainder of the file contains the aligned nucleotide sequence data for the five genes. Data partitions, representing the individual genes and different codon positions of the protein-coding genes, are indicated by the lines beginning "charset" near the end of the file. Two supplementary tables in the provided PDF file provide additional information on the species in the dataset, including the GenBank accession numbers for the sequence data (Table S1) and the DNA substitution models used for each of the data partitions used for analyses in the phylogenetic analysis program IQ-Tree (version 1.6.8) (Table S3), as described in the Methods section of the paper. The supplemental tables will also be linked to the article upon publication at the journal website.

MATLAB files for the analysis of an ODE model for disease transmission. The codes may be used to find equilibrium points, study transient dynamics, evaluate the basic reproductive number (R0), and simulate the model when parameters depend on the independent variables. In addition, the codes may be used to perform local sensitivity analysis of R0 on the model parameters.

The data contains a list of articles given low score by the RCT Tagger and an error analysis of them, which were used in a project associated with the manuscript "Evaluation of publication type tagging as a strategy to screen randomized controlled trial articles in preparing systematic reviews". Change made in this V3 is that the data is divided into two parts: - Error Analysis of 44 Low Scoring Articles with MEDLINE RCT Publication Type. - Error Analysis of 244 Low Scoring Articles without MEDLINE RCT Publication Type.

Data were used to analyze patterns in predator-specific nest predation on shrubland birds in Illinois as related to landscape composition at multiple landscape scales. Data were used in a Journal of Applied Ecology research paper of the same name. Data were collected between 2011 and 2014 at sites in east-central and northeastern Illinois, USA as part of a Ph.D. research project on the relationship between avian nest predation and landscape characteristics, and how nest predation affects adult and nestling bird behavior.