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Table 2 from Chemical Substructure Search in SQL
<p>These are queries reported in Table 2 of:</p> <p> Adel Golovin and Kim Henrick,<br> Chemical Substructure Search in SQL,<br> Journal of Chemical Information and Modeling 2009 49 (1), 22-27<br> <a href="https://doi.org/10.1021/ci8003013">https://doi.org/10.1021/ci8003013</a></p> <p>Data provenance<br> ===============</p> <p>The queries are in Table 2, located on p. 25. I extracted an image of that table and placed it in 10.1021_ci8003013_Table_2.pdf .</p> <p>The spreadsheet is in ods format, created by LibreOffice.</p> <p>I used a combination of copy&paste and manual editing/entry to create the sheet "Original" with 15 entries.</p> <p>The copy&paste from the PDF used incorrect characters, primarily regarding the double-bond '='. I fixed those, and manually verified that the fix matched the visual appearance of the original table.</p> <p>Note that one of the steroid entries is invalid, likely when a "cc" was interpreted as cm³:</p> <p> CC12CCCC1C3CCc4 cm³(O)ccc4C3CC2 steroid</p> <p>The sheet "Processed" contains the SMILES and description from sheet "Original" column A, manually split into the columns "SMILES" and "description". This table has 14 entries.</p> <p>I have taken the lead from Agrafiotis et al. in "Efficient Substructure Searching of Large Chemical Libraries" and ignored that steroid line, rather than guess the original intent.</p> <p>History<br> =======</p> <p>30 May 2014<br> -----------</p> <p>Added the transcribed entry to the SQC.</p> <p>Andrew Dalke</p> <p>26 September 2022<br> -----------------</p> <p>Updated for distribution on Zenodo.</p> <p>Andrew Dalke</p>
Table 2 from Efficient Substructure Searching of Large Chemical Libraries: The ABCD Chemical Cartridge
<p>These 46 SMARTS queries come from Table 2 of:</p> <p> Dimitris K. Agrafiotis, Victor S. Lobanov, Maxim Shemanarev,<br> Dmitrii N. Rassokhin, Sergei Izrailev, Edward P. Jaeger, Simson<br> Alex, and Michael Farnum,<br> Efficient Substructure Searching of Large Chemical Libraries: The<br> ABCD Chemical Cartridge,<br> Journal of Chemical Information and Modeling 2011 51 (12), 3113-3130<br> <a href="https://doi.org/10.1021/ci200413e">https://doi.org/10.1021/ci200413e</a></p> <p>The SMARTS queries are in Table 2 (pages 3122-3123). A copy of the original table is in 10.1021_ci200413e_Table_2.pdf .</p> <p>The LibreOffice spreadsheet file 10.1021_ci200413e.ods contains three worksheets.</p> <p>- The "Overview" sheet contains a summary of the data set.</p> <p>- The "Table 2" sheet contains the table data.</p> <p>- The "ID map" sheet contains a mapping from the labels used in Agrafiotis et al. to the labels used in the original papers.</p> <p>This dataset is derived from two other data sets:</p> <p> Chemical Substructure Search in SQL<br> Adel Golovin and Kim Henrick<br> Journal of Chemical Information and Modeling 2009 49 (1), 22-27<br> https://doi.org/10.1021/ci8003013<br> See also doi:10.5281/zenodo.7116311</p> <p> Martin G. Hicks and Clemens Jochum<br> Substructure search systems. 1. Performance comparison of the MACCS, DARC, HTSS,<br> CAS Registry MVSSS, and S4 substructure search systems<br> Journal of Chemical Information and Computer Sciences 1990 30 (2), 191-199<br> https://doi.org/10.1021/ci00066a018<br> See also doi:10.5281/zenodo.7116311</p> <p>See the README for full details.</p>
Query structures from Figure 4 of Comparison of Substructure Search Systems
<p>These 29 SMARTS queries come from Figure 4 on page 193 of:</p> <p> Martin G. Hicks and Clemens Jochum,<br> Substructure search systems. 1. Performance comparison of the<br> MACCS, DARC, HTSS, CAS Registry MVSSS, and S4 substructure search systems,<br> Journal of Chemical Information and Computer Sciences 1990 30 (2), 191-199<br> <a href="https://doi.org/10.1021/ci00066a018">https://doi.org/10.1021/ci00066a018</a></p> <p>The SMARTS queries are in Figure 4 (page 193). A copy of the original table is in 10.1021_ci00066a018_Figure_4.pdf . The LibreOffice spreadsheet file 10.1021_ci00066a018.ods contain two sheets. The "Overview" sheet gives a summary of the data set. The "Query structures" sheet contains the data from Figure 4.</p> <p>The Hicks and Jochum paper does not give the query as SMARTS strings. Instead, the queries were translated to SMARTS in the following paper:</p> <p> Dimitris K. Agrafiotis, Victor S. Lobanov, Maxim Shemanarev,<br> Dmitrii N. Rassokhin, Sergei Izrailev, Edward P. Jaeger,<br> Simson Alex, and Michael Farnum<br> Efficient Substructure Searching of Large Chemical Libraries:<br> The ABCD Chemical Cartridge<br> Journal of Chemical Information and Modeling 2011 51 (12), 3113-3130<br> <a href="https://doi.org/10.1021/ci200413e">https://doi.org/10.1021/ci200413e</a></p> <p>Two of the SMARTS patterns were changed to produce this dataset. During cross-checking with the original paper, and with the help of SMARTSviewer, I believe I identified two mistakes in the conversion, described in the README.</p>
Figure 6 from: Benayahu Y, McFadden CS, Shoham E, van Ofwegen LP (2017) Search for mesophotic octocorals (Cnidaria, Anthozoa) and their phylogeny. II. A new zooxanthellate species from Eilat, northern Red Sea. ZooKeys 676: 1-12. https://doi.org/10.3897/zookeys.676.12751
Figure 6 - Sinularia lamellata RMNH Coel no. 12864. Sclerites of the polypary. A clubs of surface layer B–C point sclerites D spindles from surface E spindles from interior F tuberculation. Scale bars: 0.10 mm (A–D, F), 1 mm (E).
Figure 2 from: Benayahu Y, McFadden CS, Shoham E, van Ofwegen LP (2017) Search for mesophotic octocorals (Cnidaria, Anthozoa) and their phylogeny. II. A new zooxanthellate species from Eilat, northern Red Sea. ZooKeys 676: 1-12. https://doi.org/10.3897/zookeys.676.12751
Figure 2 - Sinularia mesophotica sp. n., holotype ZMTAU Co 37425. Sclerites from the polypary. A tentacle rods B straight collaret spindles C bent collaret spindles D clubs E larger clubs. Scale bar: 0.10 mm.
Figure 3 from: Benayahu Y, McFadden CS, Shoham E, van Ofwegen LP (2017) Search for mesophotic octocorals (Cnidaria, Anthozoa) and their phylogeny. II. A new zooxanthellate species from Eilat, northern Red Sea. ZooKeys 676: 1-12. https://doi.org/10.3897/zookeys.676.12751
Figure 3 - Sinularia mesophotica sp. n., holotype ZMTAU Co 37425. Sclerites of the base of colony. A clubs of the surface layer B spindles of interior C tuberculation of the spindles. Scale bars: 0.10 mm (A, C), 1 mm (B).
Figure 3 from: Benayahu Y, McFadden CS, Shoham E (2017) Search for mesophotic octocorals (Cnidaria, Anthozoa) and their phylogeny: I. A new sclerite-free genus from Eilat, northern Red Sea. ZooKeys 680: 1-11. https://doi.org/10.3897/zookeys.680.12727
Figure 3 - Altumia delicata gen. n. sp. n. live colonies. A, B colonies growing over branch of black coral with expanded polyps C colonies growing on PVC net (arrow heads).
Figure 5 from: Benayahu Y, McFadden CS, Shoham E, van Ofwegen LP (2017) Search for mesophotic octocorals (Cnidaria, Anthozoa) and their phylogeny. II. A new zooxanthellate species from Eilat, northern Red Sea. ZooKeys 676: 1-12. https://doi.org/10.3897/zookeys.676.12751
Figure 5 - Maximum likelihood tree of concatenated mtMutS and igr1+COI mitochondrial gene sequences. Clade numbering system follows McFadden et al. (2009); some clades have been collapsed to facilitate readability. Asterisks indicate species with a funnel-shaped morphology similar to that of Sinularia mesophotica sp. n. Bootstrap values >50% are indicated adjacent to nodes.
Figure 1 from: Benayahu Y, McFadden CS, Shoham E (2017) Search for mesophotic octocorals (Cnidaria, Anthozoa) and their phylogeny: I. A new sclerite-free genus from Eilat, northern Red Sea. ZooKeys 680: 1-11. https://doi.org/10.3897/zookeys.680.12727
Figure 1 - Phylogenetic relationships among species of octocorals that lack sclerites (red asterisks) and members of family Clavulariidae (blue labels), including Altumia delicata gen n. sp. n. (red label). Solid circles at nodes indicate strong support from both maximum-likelihood (bootstrap value >70%) and Bayesian (posterior probability >0.90) analyses; split circles indicate strong support from one analysis only (left half solid: supported by ML; right half solid: supported by Bayesian analysis). Strongly supported clades that include no clavulariid or sclerite-free species have been collapsed. Hexacorallian outgroup taxa used to root tree are not shown. For a comprehensive list of taxa and sequences included in the analyses see McFadden and Ofwegen (2012).
Figure 2 from: Benayahu Y, McFadden CS, Shoham E (2017) Search for mesophotic octocorals (Cnidaria, Anthozoa) and their phylogeny: I. A new sclerite-free genus from Eilat, northern Red Sea. ZooKeys 680: 1-11. https://doi.org/10.3897/zookeys.680.12727
Figure 2 - Altumia delicata gen. n. sp. n. holotype ZMTAU CO 37427. A Colony growing over a branch of a black coral B close up of holotype. Scale 10 mm at A, 1 mm at B.
Figure 7 from: Benayahu Y, McFadden CS, Shoham E, van Ofwegen LP (2017) Search for mesophotic octocorals (Cnidaria, Anthozoa) and their phylogeny. II. A new zooxanthellate species from Eilat, northern Red Sea. ZooKeys 676: 1-12. https://doi.org/10.3897/zookeys.676.12751
Figure 7 - Sinularia lamellata RMNH Coel no. 12864. Sclerites of the colony base; A clubs of surface layer B–C spindles from interior base D tuberculation of spindles. Scale bars: 0.10 mm (A, D), 1 mm (B, C).
Figure 1 from: Benayahu Y, McFadden CS, Shoham E, van Ofwegen LP (2017) Search for mesophotic octocorals (Cnidaria, Anthozoa) and their phylogeny. II. A new zooxanthellate species from Eilat, northern Red Sea. ZooKeys 676: 1-12. https://doi.org/10.3897/zookeys.676.12751
Figure 1 - Sinularia mesophotica sp. n.; A Holotype ZMTAU Co 37425 B paratypes ZMTAU Co 37492. Scale bar: 1 cm (A also applies to B).
Figure 4 from: Benayahu Y, McFadden CS, Shoham E, van Ofwegen LP (2017) Search for mesophotic octocorals (Cnidaria, Anthozoa) and their phylogeny. II. A new zooxanthellate species from Eilat, northern Red Sea. ZooKeys 676: 1-12. https://doi.org/10.3897/zookeys.676.12751
Figure 4 - Underwater photographs of Sinularia mesophotica sp. n. A patch of colonies B funnel-shaped morphology of colonies.
Figure 4 in Description of the skeleton of the fossil beaked whale Messapicetus gregarius: searching potential proxies for deep-diving abilities
Figure 4. Sternum of the specimen MUSM 2548, Messapicetus gregarius, in ventral view (a) and manubrium element in anterior view (b). Horizontal solid lines indicate major break. The dashed line represents a reconstruction of the second element of the sternebra 2.
Universalism and Celtic Traditions in the Human Search for Meaning
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Assessing diversity in creating seed set for snowballing search for systematic literature review in software engineering
<p><strong><span>This set of files is complementary material used to evaluate the snowballing performance varying the seed set creation under the diversity perspective from the proposed tool. Specifically, the set of files includes a PDF with guidelines followed to replicate our seed set based on diversity characteristics and three spreadsheet that: i) presents the seed set of SLR Original; ii) describes the seed set recommended by tool; and iii) reflects the snowballing process and analysis.</span></strong></p>
Searching for the relationship between the presence, extent, location and 12-month dynamics of cardiac fibrosis and the genetic profile in patients with dilated cardiomyopathy - a pilot study
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Mass spectrometry search data associated with the manuscript "Propensity for Proto-gene Emergence in Bacteria"
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Figure 1 in Rivers in search of the European eel. Distribution and threats of the Critically Endangered Anguilla anguilla (Linnaeus, 1758) in Sicily: the province of Ragusa as a case study
Figure 1. – Distribution of the European eel Anguilla anguilla in the rivers of the Ragusa province. (D: Dirillo, A: Amerillo, Mz: Mazzarronello, Ip: Ippari, R: Rifriscolaro, I: Irminio, V: Volpe, M: Mastratto, C: Ciaramite, SL: San Leonardo, MS: Modica-Scicli, F: Favara, Tr: Tellaro, Tl: Tellesimo, Pr: Prainito; m: mortality; p: poaching).
Feature selection in an interactive search-based PLA design approach
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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)
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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.