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Dataset results
16 results for “relationship extraction”
Evaluation dataset for Relation Extraction of relationships between Organisms and Natural-Products
<p>A curated evaluation dataset for end-to-end Relation Extraction of relationships between organisms and natural-products.</p> <p>Details about the manual annotation:</p> <ul> <li>For Chemicals: <ul> <li>The chemical labels are annotated as they appear in the abstract.</li> <li>In abstracts, singular chemicals and classes of chemicals produced by a specific organism were distinguished.</li> <li>The "type" attribute {“chemical”, “class”} is used to indicate the nature of the mentioned name.</li> <li>A "class" attribute for chemical entities has also been included if class information is present in the abstract.</li> <li>A Wikidata and PubChem identifiers were assigned to chemicals and classes when available.</li> </ul> </li> <li>For Organisms: <ul> <li>The organism labels are annotated as they appear in the abstract.</li> <li>If in an abstract, the genus name was mention first, e.g. "Plakinastrella sp." and then the specie name e.g "Plakinastrella clathrata" is precise, then only the specie name is used.</li> <li>A Wikidata identifier was assigned to all organisms.</li> <li>In some abstracts, only the genus name is mentioned.</li> </ul> </li> <li>For Relations: <ul> <li>Only the relations explicitly mentioned in the abstract are reported in the output labels.</li> <li>Relations are reported in their order of appearance in the abstract.</li> </ul> </li> </ul>
Seasonal relationships between soil respiration and water-extractable carbon as influenced by soil temperature and moisture in forest soils of the Andrews Experimental Forest, 1992-1993
The overall objective of this study is to model trace gas emissions from forest soils of the H. J. Andrews Experimental Forest. This is to be accomplished by studying trace gas emissions and related variable at a set of 20 permanent plots at the HJA.
Synthetic dataset for end-to-end Relation Extraction of relationships between Organisms and Natural-Products with Vicuna-13b-v1.5
<p>A new synthetic dataset (training/validation) for end-to-end Relation Extraction of relationships between Organisms and Natural-Products.</p><p>The new dataset was generated using <a href="https://huggingface.co/lmsys/vicuna-13b-v1.5">Vicuna-13b-v1.5</a>, derived from LLaMA 2. Like the model, the produced synthetic data are also submitted to the License of the model used for generation, see the original <a href="https://github.com/facebookresearch/llama/blob/main/LICENSE">LLaMA 2 license</a>.</p><p>The new dataset was created based on the top-1000 (per biological kingdom) LOTUS literature references extracted with the <a href="https://github.com/idiap/gme-sampler">GME-sampler</a>.</p><p>The dataset contains 10,405 items in the training set and 547 items in the validation set.</p><p>The dataset was generated using the same protocol as described in the <a href="https://github.com/idiap/gme-sampler">article</a>.</p>
Synthetic dataset for end-to-end Relation Extraction of relationships between Organisms and Natural-Products with Mixtral-8x7B-Instruct-v0.1
<p>A new synthetic dataset (training/validation) for end-to-end Relation Extraction of relationships between Organisms and Natural-Products.</p> <p>The new dataset was generated using <a href="https://huggingface.co/mistralai/Mixtral-8x7B-Instruct-v0.1">Mixtral-8x7B-Instruct-v0.1</a>. Like the model, the produced synthetic data are also submitted to the License of the model used for generation (apache-2.0).</p> <p>The new dataset was created based on the top-1000 (per biological kingdom) LOTUS literature references extracted with the <a href="https://github.com/idiap/gme-sampler">GME-sampler</a>.</p> <p>The dataset contains 8,913 items in the training set and 344 items in the validation set.</p> <p>The dataset was generated using the same protocol as described in the article.</p>
Supporting material for von Fromm et al (2024) Moisture and soil depth govern relationships between soil organic carbon and oxalate-extractable metals at the global scale
<p>This file contains the supporting material for von Fromm et al (2024) Moisture and soil depth govern relationships between soil organic carbon and oxalate-extractable metals at the global scale (<em>submitted</em>). </p> <p>For more details see the corresponding manuscript (once it is published) and the github repository (https://github.com/SophievF/Global_Mox_analysis/tree/main). </p>
Relationship between Channel Island Melospiza melodia (Song Sparrow) bill size and vegetation, seed extraction time, bite force, and climate (2014-2016)
<p>Inferring the environmental selection pressures responsible for phenotypic variation is a challenge in adaptation studies as traits often have multiple functions and are shaped by complex selection regimes. We provide indirect evidence that morphology of the multifunctional avian bill is primarily shaped by climate and thermoregulatory ability in <em>Melospiza melodia</em> (Song Sparrows) on the California Channel Islands. Our research builds on a study in Song Sparrow museum specimens that demonstrated a positive correlation between bill surface area and maximum temperature, suggesting a greater demand for dry heat dissipation in hotter, xeric environments. We sampled contemporary sparrow populations across three climatically distinct islands to test the hypotheses that bill morphology is influenced by habitat differences with functional consequences for foraging efficiency and is related to maximum temperature and, consequently, important for thermoregulation. Measurements of >500 live individuals indicated a significant, positive relationship between maximum temperature and bill surface area when correcting for body size. In contrast, maximum bite force, seed extraction time, and vegetation on breeding territories (a proxy for food resources) were not significantly associated with bill dimensions. While we cannot exclude the influence of foraging ability and diet on bill morphology, our results are consistent with the hypothesis that variation in Song Sparrows' need for thermoregulatory capacity across the northern Channel Islands selects for divergence in bill surface area.</p>
Synthetic datasets for end-to-end Relation Extraction of relationships between Organisms and Natural-Products
<p>Synthetic datasets (training/validation) for end-to-end Relation Extraction of relationships between Organisms and Natural-Products. The datasets are provided for reproducibility purposes, but, can also be used to train new models.</p><p>As in the corresponding article, 3 subtypes of synthetic datasets are provided:</p><ul><li><i>Diversity-synt</i>:<strong> </strong>The seed literature references used in the generation process correspond to the top-500 extracted items per biological kingdoms using the <a href="https://github.com/idiap/gme-sampler">GME-sampler</a>.</li><li><i>Random-synt</i>:<strong> </strong>5 datasets of equivalent sizes as <i>Diversity-synt</i>, but using randomly sampled seed literature references.</li><li><i>Extended-synt</i>: A merge of <i>Diversity-synt and the 5 Random-synt datasets.</i><br> </li></ul><p><strong>All </strong>datasets were produced with <a href="https://huggingface.co/lmsys/vicuna-13b-v1.3">Vicuna-13b-v1.3</a>. Like the model, the produced synthetic data are also submitted to the License of the model used for generation, see the original <a href="https://github.com/facebookresearch/llama/blob/llama_v1/MODEL_CARD.md">LLaMA model card</a>.</p><p>LLaMA is licensed under the <a href="https://github.com/facebookresearch/llama/blob/llama_v1/MODEL_CARD.md">LLaMA License</a>, Copyright (c) Meta Platforms, Inc. All Rights Reserved. </p>
Relationship between Channel Island Melospiza melodia (Song Sparrow) bill size and vegetation, seed extraction time, bite force, and climate (2014-2016)
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Data compilation for project Ground vertical displacement and its relationship with injection and extraction of fluids in North Louisiana
<p>This repository contains the database for the project "Ground vertical displacement and its relationship with injection and extraction of fluids in North Louisiana". This is the third chapter of the PhD thesis of Hurtado-Pulido</p> <p>Authors: Hurtado-Pulido C., Ebinger, C.</p> <p>The datasets used in this project were compiled and curated by Hurtado-Pulido from different sources for her PhD dissertation. <br>Earthquakes in the ISLA dataset were collected during the ISLA project (2019-2022), which was led by Ebinger (the Project's PI).</p> <p>If you use this dataset or part of it please also cite the original references listed in the READme document.</p> <p>Please address any questions about this dataset to Hurtado-Pulido.</p>
Relationship Between Magnesium Depletion Score and Extraction Socket Healing
ClinicalTrials.gov study NCT06891846. IPD Sharing: NO. Countries: 1. Publications: 5.
Data from: Extracting phylogenetic signal from phylogenomic data: higher-level relationships of the nightbirds (Strisores)
A well-resolved phylogeny would facilitate study of adaptation to nocturnality in the avian superorder Strisores, a group that includes both nocturnal and diurnal lineages. Based on previous estimates, it could be hypothesized that there were multiple independent origins of nocturnality in this group. In order to refine the Strisores phylogeny, we generated genome-scale datasets of 2,289 – 4,243 ultra-conserved elements for 23 taxa representing all major living lineages in the group. Among the considerations for using genome-scale, molecular sequence data in phylogenomic analysis are issues related to GC content, GC variance and their effects on model selection. In this study, we employed a variety of analytical techniques to empirically investigate those issues in our data, as well as biases and errors resulting from alignment trimming, taxon selection and matrix completeness. Extensive analyses revealed conflict within the data, especially in regard to variation in GC content, that would not have been detected with more cursory study. Our results indicate that readily available models of molecular evolution are insufficient to encapsulate all phenomena present in genome-scale matrices, and that this problem may be at the root of many current issues in phylogenomic analysis. The analytical methods employed in this study are relevant to phylogenomic analysis of any large, heterogeneous matrix. In conclusion, we present a strongly supported estimate of the Strisores tree and discuss potential evolutionary pathways of nocturnality in this clade.
Relationship between mineral extraction, oil extraction, and agribusiness with employability, municipal gross domestic product, and voting data in Brazil
<p>This dataset looks at the number of Brazilian municipalities where mining is a key economic activity and those where mining is a key job provider. We also listed municipalities that have mining as both a main economic activity and the main employer in a given town. We have also generated maps to visualize the impact of mining in Brazil as a key economic activity and/or job provider. Similarly, we have listed the same information for all the municipalities that received oil royalties in 2019, and the top 100 municipalities whose wealth was mainly generated by agribusiness in 2022. By detailing the economic and employment situation in Brazilian extractive municipalities (mining, oil, and crops), we demonstrate that company towns in Brazil (locations that are highly dependent on one key economic activity for employment generation) are few. Extractive industries may no longer be labour intensive, although economic dependency may follow indirectly, such as because of tax generation. We also offer data on national elections to demonstrate that there is not a clear correlation between economic activity and voting patterns, which may be explained by low employability. The main objective of this dataset is to generate a discussion on the need to redefine company towns in Brazil.</p>
Relationship between mineral extraction, oil extraction, and agribusiness with employability, municipal gross domestic product, and voting data in Brazil
Open the record for dataset details and reuse information.
Data from: Extracting phylogenetic signal from phylogenomic data: higher-level relationships of the nightbirds (Strisores)
Open the record for dataset details and reuse information.
Relationship Between Methods of Bladder Tumor Extraction and Local Recurrence Rate
ClinicalTrials.gov study NCT04750590. IPD Sharing: NO. Countries: 1. Publications: 0.
Dataset: Relationship extraction for knowledge graph creation from biomedical literature (Gene-Disease relationships)
<p>This is the dataset used for classifying Gene-Disease relationship types from sentences. The dataset consists of 3 files:</p> <ul> <li>manually_annotated_set.xlsx - set of 2000 manualy annotated sentences with entities</li> <li>Unbalanced_dataset.xlsx - set of 12000 sentences, out of which 2000 are from the first set, manually annotated, and the rest have been added using rule based method by adding sentences where extraction had confidence 1.</li> <li>Balanced_dataset_SUB_PRED.xlsx - balanced dataset generated by taking 2000 manually annotated sentences, but then adding sentences from the rule-based method with confidence 1 in such a way that each relationship class had at least 1400 sentences (for biomarkers, we could obtain 1243 sentences with confidence 1 from a processed portion of the data we had at the time of building the dataset).</li> </ul> <p> </p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.