Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
182
datasets available to search
ShareScore release 0.9.0
Dataset results
182 results for “molecular collections”
A collection of molecular formula databases for HERMES
<p>A compilation of different molecule databases ready to be used in <a href="https://www.biorxiv.org/content/10.1101/2021.03.08.434466v1">HERMES</a>. We have compiled different open-access DBs and adapted their format to the HERMES requisite columns. Since all databases share the "Name" and "MolecularFormula" columns, merges between databases can be easily generated.</p> <p>More databases and merges will be added in the future. If you have any suggestions or want to contribute, feel free to contact us!</p> <p>All rights reserved to the original authors of the databases.</p> <p>Description of the files:</p> <ul> <li>ECMDB.csv: Entries from <a href="https://ecmdb.ca/"><em>E. coli</em> Metabolome Database</a>. 3760 compounds.</li> <li>Merge_KEGG_ECMDB.csv: a merge between all metabolites from <a href="https://www.genome.jp/kegg/pathway.html">KEGG pathways</a> associated to E.coli K12 with the ECMDB.csv from above. 6107 compounds.</li> <li>Merge_LipidMaps_LipidBlast.csv: a merge between lipid entities from <a href="https://www.lipidmaps.org/resources/databases/index.php">LipidMaps</a> LMSD and the metadata (just Name and Molecular Formula) of <a href="https://fiehnlab.ucdavis.edu/projects/LipidBlast">LipidBlast</a> entries. 163453 compounds.</li> <li>norman.xls: Entries from <a href="https://www.norman-network.com/nds/susdat/susdatSearchShow.php">NORMAN SusDat</a>, containing common and emerging drugs, pollutants, etc. 52019 compounds.</li> <li>PubChemLite_31Oct2020.csv Adapted column names from <a href="https://zenodo.org/record/4183801">https://zenodo.org/record/4183801</a>. 371,663 compounds related to exposomics.</li> <li>MS1_2ID.csv. Merge of HMDB, ChEBI and NORMAN compounds. 183911 compounds related to Human Metabolism, drugs, etc..</li> <li>COCONUT_NP.csv: parsed collection of entries from the COlleCtion of Open Natural ProdUcTs (<a href="https://coconut.naturalproducts.net/">COCONUT</a>).406752 compounds.</li> <li>DiTriPeptides.csv: a list of all theoretically possible dipeptides (400) and tripeptides (8000) and their associated molecular formulas. 8400 compounds.</li> </ul>
Figure 1 in Molecular detection of Borrelia anserina in Argas persicus (Acari: Argasidae) ticks collected from Lorestan province, west of Iran
Figure 1. The aggregated Argas persicus ticks at different stages around a thatched birdhouse in Lorestan province.
Figure 3 in Molecular detection of Borrelia anserina in Argas persicus (Acari: Argasidae) ticks collected from Lorestan province, west of Iran
Figure 3. The phylogenetic tree inferred from flaB amino acids sequence data of B. anserina (clade I) and other Borrelia taxa (clade II, KX171816 and JF693808) constructed using Neighbor-Joining (NJ) method with bootstrap test (1,000 replicates). The main clade in right side of tree separated with colored rectangular shape. Taxa are as species name following GenBank accession number, taxon of the present study indicated as bold. Nodes indicated with bootstrap value. Branch lengths are proportional to evolutionary changes, the units of the number of amino acid substitutions per site. The analysis involved 12 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 166 positions in the final dataset. The more diverged Pakistani strain of B. anserina (JF693808) located outside the main B. anserina (clade I). The members of clade II and B. hermsii are as outgroup.
Figure 2 in Molecular detection of Borrelia anserina in Argas persicus (Acari: Argasidae) ticks collected from Lorestan province, west of Iran
Figure 2. The stereomicroscopic view of dissected salivary glands (A); ovary and uterus (B) of female Argas tick in normal saline.
Figure 4 in Molecular detection of Borrelia anserina in Argas persicus (Acari: Argasidae) ticks collected from Lorestan province, west of Iran
Figure 4. The phylogenetic tree inferred from flaB nucleotide sequence data of B. anserina (clade I) and other Borrelia taxa (clade II and KX171816) constructed using Neighbor-Joining (NJ) method with bootstrap test (1000 replicates). The main clade in right side of tree separated with colored rectangular shape. Taxa are as species name following GenBank accession number, taxon of the present study indicated as bold. Nodes indicated with bootstrap value. Branch lengths are proportional to evolutionary changes, the units of the number of base substitutions per site the units of the number of amino acid substitutions per site. The analysis involved 12 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 500 positions in the final dataset. The more diverged Pakistani strain of B. anserina (JF693808) located inside the main B. anserina (clade I). The members of clade II and B. hermsii are as outgroup.
Figure 10 in Morphological and molecular identification of Cladosporium sphaerospermum isolates collected from tomato plant residues
Figure 10. Nucleotide sequence alignment of the ITS (ITS1, 5.8S rDNA and ITS4) region of the C. sphaerospermum isolate 10 and the other isolates already recorded in NCBI.
Figure 8 in Morphological and molecular identification of Cladosporium sphaerospermum isolates collected from tomato plant residues
Figure 8. Nucleotide sequence alignment of the ITS (ITS1, 5.8S rDNA and ITS4) region of the C. sphaerospermum isolate 9 and the other isolates already recorded in NCBI.
Figure 5. A phylogenetic tree was generated using the neighbor-joining method which shows the genetic relationship between C. sphaerospermum 2 in Morphological and molecular identification of Cladosporium sphaerospermum isolates collected from tomato plant residues
Figure 5. A phylogenetic tree was generated using the neighbor-joining method which shows the genetic relationship between C. sphaerospermum 2 (as indicated in red circle) and the other C. sphaerospermum isolates deposited in GenBank (NCBI)
Figure 3. A in Morphological and molecular identification of Cladosporium sphaerospermum isolates collected from tomato plant residues
Figure 3. A phylogenetic tree constructed by the neighbor-joining method depending on a comparison of the nucleotide sequences obtained from the C. sphaerospermum isolates (1-13).
Figure 2 in Morphological and molecular identification of Cladosporium sphaerospermum isolates collected from tomato plant residues
Figure 2. The similarity and difference in the nucleotide sequences of the C. sphaerospermum isolates (1-13) identified in the present study. Similar nucleotides are stated in dots. Numbers given on the right side of the figure represent the nucleotide sequences obtained from the C. sphaerospermum isolates.
Figure 1. 1 in Morphological and molecular identification of Cladosporium sphaerospermum isolates collected from tomato plant residues
Figure 1. 1% Agarose gel electrophoresis of PCR products amplified using the primer pair ITS1 and ITS4 from the C. sphaerospermum isolates (1-13) obtained from tomato plant residues collected from different regions of Najaf and Karbala provinces. M: 1Kbp DNA Ladder (Promega, USA).
Fig. 14 in Molecular Identification of Mid to Final Stage Slipper Lobster Phyllosoma Larvae of the Genus (Crustacea: Decapoda: Scyllaridae) Collected in the Pacific with Descriptions of Their Larval Morphology.
Fig. 14. Phyllosoma larva of?Chelarctus sp-1, stage VII. A, ventral view; B, ventral view of eye, antennule and antenna; C, 2nd maxillule, 1st and 2nd maxilliped; D, distal end of 2nd maxilliped; E ventral view of 1st maxillule; F, ventral view of 5th pereiopod and abdomen; G, dorsal view of 5th pereiopod and abdomen.
Fig. 11 in Molecular Identification of Mid to Final Stage Slipper Lobster Phyllosoma Larvae of the Genus (Crustacea: Decapoda: Scyllaridae) Collected in the Pacific with Descriptions of Their Larval Morphology.
Fig. 11. Phyllosoma larva of Chelarctus crosnieri sub sp., stage V. A, ventral view; B, ventral view of eye, antennule and antenna; C, 2nd maxillule, 1st and 2nd maxilliped; D, distal end of 2nd maxilliped; E, ventral view of 1st maxillule; F, ventral view of 5th pereiopod and abdomen; G, dorsal view of 5th pereiopod and abdomen.
Fig. 5 in Molecular Identification of Mid to Final Stage Slipper Lobster Phyllosoma Larvae of the Genus (Crustacea: Decapoda: Scyllaridae) Collected in the Pacific with Descriptions of Their Larval Morphology.
Fig. 5. Phyllosoma larva of Chelarctus virgosus, stage VI. A, ventral view; B, ventral view of eye, antennule and antenna; C, 2nd maxillule, 1st and 2nd maxilliped; D, distal end of 2nd maxilliped; E, ventral view of 1st maxillule; F, ventral view of 5th pereiopod and abdomen; G, dorsal view of 5th pereiopod and abdomen.
Fig. 4 in Molecular Identification of Mid to Final Stage Slipper Lobster Phyllosoma Larvae of the Genus (Crustacea: Decapoda: Scyllaridae) Collected in the Pacific with Descriptions of Their Larval Morphology.
Fig. 4. Phyllosoma larva of Chelarctus virgosus, stage V. A, ventral view; B, ventral view of eye, antennule and antenna; C, 2nd maxillule, 1st and 2nd maxilliped; D, distal end of 2nd maxilliped; E ventral view of 1st maxillule; F, ventral view of 5th pereiopod and abdomen; G, dorsal view of 5th pereiopod and abdomen.
Fig. 2 in Molecular Identification of Mid to Final Stage Slipper Lobster Phyllosoma Larvae of the Genus (Crustacea: Decapoda: Scyllaridae) Collected in the Pacific with Descriptions of Their Larval Morphology.
Fig. 2. Neighbor-joining phylogenetic tree drawn using the Kimura-2-parameter distances for each of the partial COI sequences between the subfamily Scyllarinae species. Scyllarides brasiliensis was used as the outgroup. Closed squares indicate the phyllosoma specimens analyzed in this study. Bootstrap values of> 50% (from 1000 replicates) are shown at each node.
Fig. 1 in Molecular Identification of Mid to Final Stage Slipper Lobster Phyllosoma Larvae of the Genus (Crustacea: Decapoda: Scyllaridae) Collected in the Pacific with Descriptions of Their Larval Morphology.
Fig. 1. Survey area and collection locations for the phyllosoma larvae sampled by the three research vessels: RV Shunyo-maru (SHU), Koyo-maru (KY), and RV Hakuho-maru (KH). Closed red circles indicate the sampling stations where Scyllarinae phyllosomas were collected. The specimens analyzed in this study were collected from the large circle stations. See table 1 for specimen ID.
Fig. 13 in Molecular Identification of Mid to Final Stage Slipper Lobster Phyllosoma Larvae of the Genus (Crustacea: Decapoda: Scyllaridae) Collected in the Pacific with Descriptions of Their Larval Morphology.
Fig. 13. Phyllosoma larva of?Chelarctus sp-1, stage VI. A, ventral view; B, ventral view of eye, antennule and antenna; C, 2nd maxillule, 1st and 2nd maxilliped; D, distal end of 2nd maxilliped; E, ventral view of 1st maxillule; F, ventral view of 5th pereiopod and abdomen; G, dorsal view of 5th pereiopod and abdomen.
Fig. 3 in Molecular Identification of Mid to Final Stage Slipper Lobster Phyllosoma Larvae of the Genus (Crustacea: Decapoda: Scyllaridae) Collected in the Pacific with Descriptions of Their Larval Morphology.
Fig. 3. Neighbor-joining phylogenetic tree drawn using the Kimura-2-parameter distances for each of the partial 16S rDNA sequences for species belonging to the subfamily Scyllarinae. Scyllarides brasiliensis was used as the outgroup. Closed squares indicate the phyllosoma specimens analyzed in this study. Bootstrap values of> 50% (from 1000 replicates) are shown at each node.
Fig. 7 in Molecular Identification of Mid to Final Stage Slipper Lobster Phyllosoma Larvae of the Genus (Crustacea: Decapoda: Scyllaridae) Collected in the Pacific with Descriptions of Their Larval Morphology.
Fig. 7. Phyllosoma larva of Chelarctus virgosus, stage VIII. A, ventral view; B, ventral view of eye, antennule and antenna; C, 2nd maxillule, 1st and 2nd maxilliped; D, distal end of 2nd maxilliped; E ventral view of 1st maxillule; F, ventral view of 5th pereiopod and abdomen; G, dorsal view of 5th pereiopod and abdomen.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.