cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.60712/si-id60605.1
title: StrainInfo SI-ID 60605.1

description: StrainInfo dataset 60605 about a strain of Pseudomonas. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60606.1
title: StrainInfo SI-ID 60606.1

description: StrainInfo dataset 60606 about a strain of Methylophilus methylotrophus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60607.1
title: StrainInfo SI-ID 60607.1

description: StrainInfo dataset 60607 about a strain of Pseudomonas aeruginosa. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60702.1
title: StrainInfo SI-ID 60702.1

description: StrainInfo dataset 60702 about a strain of Rhodococcus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60703.1
title: StrainInfo SI-ID 60703.1

description: StrainInfo dataset 60703 about a strain of Pseudomonas. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.6084/m9.figshare.25398247
title: Supplementary data to the paper: Transcription factor prediction using protein 3D secondary structures

description: <b>Motivation</b>: Transcription factors (TFs) are DNA-binding proteins that regulate gene expression. Traditional methods predict a protein as a TF if the protein contains any DNA-binding domains (DBDs) of known TFs. However, this approach fails to identify a novel TF that does not contain any known DBDs. Recently proposed TF prediction methods do not rely on DBDs. Such methods use features of protein sequences to train a machine learning model, and then use the trained model to predict whether a protein is a TF or not. Because 3-dimensional (3D) structure of a protein captures more information than its sequence, using 3D protein structures will likely allow for more accurate prediction of novel TFs. <br><br>Results: We propose a deep learning-based TF prediction method (<i>StrucTFactor</i>), which is the first method to utilize 3D secondary structural information of proteins. We compare StrucTFactor with recent state-of-the-art TF prediction methods based on ∼525 000 proteins across 12 datasets, capturing different aspects of data bias (including sequence redundancy) possibly influencing a method’s performance. We find that StrucTFactor significantly (<i>p</i>-value &lt; 0.001) outperforms the existing TF prediction methods, improving the performance over its closest competitor by up to 17% based on Matthews correlation coefficient.
DOI: 10.6084/m9.figshare.25398247.v2
title: Supplementary data to the paper: Transcription factor prediction using protein 3D secondary structures

description: <b>Motivation</b>: Transcription factors (TFs) are DNA-binding proteins that regulate gene expression. Traditional methods predict a protein as a TF if the protein contains any DNA-binding domains (DBDs) of known TFs. However, this approach fails to identify a novel TF that does not contain any known DBDs. Recently proposed TF prediction methods do not rely on DBDs. Such methods use features of protein sequences to train a machine learning model, and then use the trained model to predict whether a protein is a TF or not. Because 3-dimensional (3D) structure of a protein captures more information than its sequence, using 3D protein structures will likely allow for more accurate prediction of novel TFs. <br><br>Results: We propose a deep learning-based TF prediction method (<i>StrucTFactor</i>), which is the first method to utilize 3D secondary structural information of proteins. We compare StrucTFactor with recent state-of-the-art TF prediction methods based on ∼525 000 proteins across 12 datasets, capturing different aspects of data bias (including sequence redundancy) possibly influencing a method’s performance. We find that StrucTFactor significantly (<i>p</i>-value &lt; 0.001) outperforms the existing TF prediction methods, improving the performance over its closest competitor by up to 17% based on Matthews correlation coefficient.
DOI: 10.60712/si-id60704.1
title: StrainInfo SI-ID 60704.1

description: StrainInfo dataset 60704 about a strain of Acinetobacter. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.6084/m9.figshare.25398247.v1
title: Supplementary data to the paper: Transcription factor prediction using protein 3D structures

description: <b>Motivation:</b> Transcription factors (TFs) are DNA-binding proteins that regulate expressions of genes in an organism. Hence, it is important to identify novel TFs. Traditionally, novel TFs have been identified by their sequence similarity to the DNA-binding domains (DBDs) of known TFs. However, this approach can miss to identify a novel TF that is not sequence similar to any of the known DBDs. Hence, computational methods have been developed for the TF prediction task that do not rely on known DBDs. Such existing methods use protein sequences to train a machine learning model, in order to capture sequence patterns of known TFs, and then use the trained model to predict novel TFs. Because 3-dimensional (3D) structure of a protein captures more functional characteristics of the protein than its sequence, using 3D protein structures can more correctly predict novel TFs.<b>Results:</b> We propose a protein 3D structure-based deep convolutional neural network pipeline (named <i>StrucTFactor</i>) for TF predictions and compare it with the existing state-of-the-art TF prediction method that relies only on protein sequences. We use 12 datasets capturing different aspects of data bias (including sequence redundancy and 3D protein structural quality) that can influence the training of a machine learning model, spanning ~550,000 proteins. We find that, over all datasets, StrucTFactor significantly (<i>p</i>-value &lt; 0.001) outperforms the existing state-of-the-art method for TF prediction, showing performance differences of up to 23% based on Matthews correlation coefficient. Our results show the importance of using 3D protein structures in the TF prediction task. We provide the StrucTFactor computational pipeline for the scientific community.
DOI: 10.60712/si-id60705.1
title: StrainInfo SI-ID 60705.1

description: StrainInfo dataset 60705 about a strain of Pseudomonas. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60545.1
title: StrainInfo SI-ID 60545.1

description: StrainInfo dataset 60545 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60546.1
title: StrainInfo SI-ID 60546.1

description: StrainInfo dataset 60546 about a strain of Pseudomonas fluorescens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60547.1
title: StrainInfo SI-ID 60547.1

description: StrainInfo dataset 60547 about a strain of Escherichia coli. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60548.1
title: StrainInfo SI-ID 60548.1

description: StrainInfo dataset 60548 about a strain of Pseudomonas putida. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60608.1
title: StrainInfo SI-ID 60608.1

description: StrainInfo dataset 60608 about a strain of Pseudomonas aeruginosa. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60609.1
title: StrainInfo SI-ID 60609.1

description: StrainInfo dataset 60609 about a strain of Bacillus cereus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60610.1
title: StrainInfo SI-ID 60610.1

description: StrainInfo dataset 60610 about a strain of Desulfovibrio multispirans. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60611.1
title: StrainInfo SI-ID 60611.1

description: StrainInfo dataset 60611 about a strain of Desulfovibrio. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.15468/dl.5c8r9z
title: Occurrence Download

description: A dataset containing 74150 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Fiocruz/COLFLEB - Coleção de Flebotomíneos"
 ]
}

 The dataset includes 74150 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0079688-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60712/si-id60707.1
title: StrainInfo SI-ID 60707.1

description: StrainInfo dataset 60707 about a strain of Thermoleophilum minutum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60708.1
title: StrainInfo SI-ID 60708.1

description: StrainInfo dataset 60708 about a strain of Rhodococcus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60709.1
title: StrainInfo SI-ID 60709.1

description: StrainInfo dataset 60709 about a strain of Rhodococcus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60710.1
title: StrainInfo SI-ID 60710.1

description: StrainInfo dataset 60710 about a strain of Rhodococcus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60549.1
title: StrainInfo SI-ID 60549.1

description: StrainInfo dataset 60549 about a strain of Aerococcus viridans. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60550.1
title: StrainInfo SI-ID 60550.1

description: StrainInfo dataset 60550 about a strain of Desulfovibrio vulgaris subsp. vulgaris. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60551.1
title: StrainInfo SI-ID 60551.1

description: StrainInfo dataset 60551 about a strain of Serratia marcescens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60612.1
title: StrainInfo SI-ID 60612.1

description: StrainInfo dataset 60612 about a strain of Enterobacter cloacae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60613.1
title: StrainInfo SI-ID 60613.1

description: StrainInfo dataset 60613 about a strain of Escherichia coli. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60614.1
title: StrainInfo SI-ID 60614.1

description: StrainInfo dataset 60614 about a strain of Limosilactobacillus fermentum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60615.1
title: StrainInfo SI-ID 60615.1

description: StrainInfo dataset 60615 about a strain of Clostridium sporogenes. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60711.1
title: StrainInfo SI-ID 60711.1

description: StrainInfo dataset 60711 about a strain of Escherichia coli. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60712.1
title: StrainInfo SI-ID 60712.1

description: StrainInfo dataset 60712 about a strain of Rahnella aquatilis. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60713.1
title: StrainInfo SI-ID 60713.1

description: StrainInfo dataset 60713 about a strain of Micromonospora parva. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60765.1
title: StrainInfo SI-ID 60765.1

description: StrainInfo dataset 60765 about a strain of Obesumbacterium proteus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60616.1
title: StrainInfo SI-ID 60616.1

description: StrainInfo dataset 60616 about a strain of Bradyrhizobium oligotrophicum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60617.1
title: StrainInfo SI-ID 60617.1

description: StrainInfo dataset 60617 about a strain of Hyphomicrobium. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60618.1
title: StrainInfo SI-ID 60618.1

description: StrainInfo dataset 60618 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60621.1
title: StrainInfo SI-ID 60621.1

description: StrainInfo dataset 60621 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60715.1
title: StrainInfo SI-ID 60715.1

description: StrainInfo dataset 60715 about a strain of Escherichia coli. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60716.1
title: StrainInfo SI-ID 60716.1

description: StrainInfo dataset 60716 about a strain of Pseudomonas putida. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60717.1
title: StrainInfo SI-ID 60717.1

description: StrainInfo dataset 60717 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60719.1
title: StrainInfo SI-ID 60719.1

description: StrainInfo dataset 60719 about a strain of Bacillus pumilus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60766.1
title: StrainInfo SI-ID 60766.1

description: StrainInfo dataset 60766 about a strain of Obesumbacterium proteus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60767.1
title: StrainInfo SI-ID 60767.1

description: StrainInfo dataset 60767 about a strain of Obesumbacterium proteus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60768.1
title: StrainInfo SI-ID 60768.1

description: StrainInfo dataset 60768 about a strain of Obesumbacterium proteus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.15468/dl.acaktx
title: Occurrence Download

description: A dataset containing 6375 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Sphaeropteris medullaris (G.Forst.) Bernh.)"
 ]
}

 The dataset includes 6375 records from 82 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0079713-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60712/si-id60622.1
title: StrainInfo SI-ID 60622.1

description: StrainInfo dataset 60622 about a strain of Pseudomonas fluorescens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60769.1
title: StrainInfo SI-ID 60769.1

description: StrainInfo dataset 60769 about a strain of Obesumbacterium proteus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60623.1
title: StrainInfo SI-ID 60623.1

description: StrainInfo dataset 60623 about a strain of Shewanella putrefaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60624.1
title: StrainInfo SI-ID 60624.1

description: StrainInfo dataset 60624 about a strain of Citrobacter freundii. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60625.1
title: StrainInfo SI-ID 60625.1

description: StrainInfo dataset 60625 about a strain of Serratia marcescens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60720.1
title: StrainInfo SI-ID 60720.1

description: StrainInfo dataset 60720 about a strain of Bacillus subtilis subsp. subtilis. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60721.1
title: StrainInfo SI-ID 60721.1

description: StrainInfo dataset 60721 about a strain of Escherichia coli. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60722.1
title: StrainInfo SI-ID 60722.1

description: StrainInfo dataset 60722 about a strain of Vibrio. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60770.1
title: StrainInfo SI-ID 60770.1

description: StrainInfo dataset 60770 about a strain of Salmonella enterica serovar Hadar. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id60771.1
title: StrainInfo SI-ID 60771.1

description: StrainInfo dataset 60771 about a strain of Salmonella enterica. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.