cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc200tql
title: CCDC 1847839: Experimental Crystal Structure Determination

description: Related Article: Guangyin Qian, Miao Bai, Shijun Gao, Han Chen, Siwei Zhou, Hong-Gang Cheng, Wei Yan, Qianghui Zhou|2018|Angew.Chem.,Int.Ed.|57|10980|doi:10.1002/anie.201806780
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc200tsn
title: CCDC 1847841: Experimental Crystal Structure Determination

description: Related Article: Guangyin Qian, Miao Bai, Shijun Gao, Han Chen, Siwei Zhou, Hong-Gang Cheng, Wei Yan, Qianghui Zhou|2018|Angew.Chem.,Int.Ed.|57|10980|doi:10.1002/anie.201806780
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc200ttp
title: CCDC 1847842: Experimental Crystal Structure Determination

description: Related Article: Guangyin Qian, Miao Bai, Shijun Gao, Han Chen, Siwei Zhou, Hong-Gang Cheng, Wei Yan, Qianghui Zhou|2018|Angew.Chem.,Int.Ed.|57|10980|doi:10.1002/anie.201806780
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1kxbkc
title: CCDC 1457203: Experimental Crystal Structure Determination

description: Related Article: Prithiviraj Khakhlary,  Munendra P. Singh,  Arnav Bhuyan,  Jubaraj B. Baruah|2018|Chem. Sel.|3|7983|doi:10.1002/slct.201801263
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1kxbld
title: CCDC 1457204: Experimental Crystal Structure Determination

description: Related Article: Prithiviraj Khakhlary,  Munendra P. Singh,  Arnav Bhuyan,  Jubaraj B. Baruah|2018|Chem. Sel.|3|7983|doi:10.1002/slct.201801263
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1kxbmf
title: CCDC 1457205: Experimental Crystal Structure Determination

description: Related Article: Prithiviraj Khakhlary,  Munendra P. Singh,  Arnav Bhuyan,  Jubaraj B. Baruah|2018|Chem. Sel.|3|7983|doi:10.1002/slct.201801263
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1kxbng
title: CCDC 1457206: Experimental Crystal Structure Determination

description: Related Article: Prithiviraj Khakhlary,  Munendra P. Singh,  Arnav Bhuyan,  Jubaraj B. Baruah|2018|Chem. Sel.|3|7983|doi:10.1002/slct.201801263
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1prckc
title: CCDC 1571593: Experimental Crystal Structure Determination

description: Related Article: Dmitrii M. Roitershtein, Lada N. Puntus, Alexander A. Vinogradov, Konstantin A. Lyssenko, Mikhail E. Minyaev, Mikhail D. Dobrokhodov, Ilya V. Taidakov, Evgenia A. Varaksina, Andrei V. Churakov, Ilya E. Nifant’ev|2018|Inorg.Chem.|57|10199|doi:10.1021/acs.inorgchem.8b01405
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc202xjk
title: CCDC 1849848: Experimental Crystal Structure Determination

description: Related Article: Haley Albright, Hannah L. Vonesh, Marc R. Becker, Brandon W. Alexander, Jacob R. Ludwig, Ren A. Wiscons, Corinna S. Schindler|2018|Org.Lett.|20|4954|doi:10.1021/acs.orglett.8b02086
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2031x3
title: CCDC 1849984: Experimental Crystal Structure Determination

description: Related Article: Masataka Umetani, Takayuki Tanaka, Atsuhiro Osuka|2018|Chemical Science|9|6853|doi:10.1039/C8SC02739K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc203218
title: CCDC 1849988: Experimental Crystal Structure Determination

description: Related Article: Masataka Umetani, Takayuki Tanaka, Atsuhiro Osuka|2018|Chemical Science|9|6853|doi:10.1039/C8SC02739K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc20323b
title: CCDC 1849990: Experimental Crystal Structure Determination

description: Related Article: Masataka Umetani, Takayuki Tanaka, Atsuhiro Osuka|2018|Chemical Science|9|6853|doi:10.1039/C8SC02739K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc20324c
title: CCDC 1849991: Experimental Crystal Structure Determination

description: Related Article: Masataka Umetani, Takayuki Tanaka, Atsuhiro Osuka|2018|Chemical Science|9|6853|doi:10.1039/C8SC02739K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc20325d
title: CCDC 1849992: Experimental Crystal Structure Determination

description: Related Article: Masataka Umetani, Takayuki Tanaka, Atsuhiro Osuka|2018|Chemical Science|9|6853|doi:10.1039/C8SC02739K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc20326f
title: CCDC 1849993: Experimental Crystal Structure Determination

description: Related Article: Masataka Umetani, Takayuki Tanaka, Atsuhiro Osuka|2018|Chemical Science|9|6853|doi:10.1039/C8SC02739K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc20327g
title: CCDC 1849994: Experimental Crystal Structure Determination

description: Related Article: Masataka Umetani, Takayuki Tanaka, Atsuhiro Osuka|2018|Chemical Science|9|6853|doi:10.1039/C8SC02739K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc20328h
title: CCDC 1849995: Experimental Crystal Structure Determination

description: Related Article: Masataka Umetani, Takayuki Tanaka, Atsuhiro Osuka|2018|Chemical Science|9|6853|doi:10.1039/C8SC02739K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc20329j
title: CCDC 1849996: Experimental Crystal Structure Determination

description: Related Article: Masataka Umetani, Takayuki Tanaka, Atsuhiro Osuka|2018|Chemical Science|9|6853|doi:10.1039/C8SC02739K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.1322710
title: Identifier Refinery Conversion Matrixes

description: <strong>identifier-refinery</strong>

Tools and assets for easy and reproducable gene identifier conversion.

<strong>Methods</strong>

This repository is used to build matricies which can convert between different gene identifiers.

These conversion matricies are built by:


	Randomly choosing raw CEL files from NCBI GEO for a given platform accession code (in <code>/cels</code>)
	Reading the CEL header and joining Brainarray (e.g., <code>hgu133plus2hsensgprobe</code>) and Bioconductor (e.g., <code>hgu133plus2.db</code>) (x, y) coordinates
	Finding intersecting probe identifiers
	Extracting supported identifiers and probe IDs from the Bioconductor package
	Filtering on probe IDs and Ensembl Gene IDs in Brainarray
	Writing the output to a conversion TSV file
	Check that all output conversion TSV files have a shared SHA1


<strong>Repository Contents</strong>

<strong>Source Files</strong>

The <code>cels</code> directory contains raw CEL files taken from GEO. The list of supported platforms is in <code>supported_microarray_platforms.csv</code>. Source files can be acquired by running the <code>acquire_cels.py</code> script.

<strong>Docker Image</strong>

The conversion scripts are run on custom Docker images.

Two Dockerfiles are provided in this repository - <code>base</code> Docker image, which is used to install the quire R dependancies, and the <code>pd</code> image, which is used to build the required databases for a given platform.

<strong>Conversion Scripts</strong>

A <code>build_and_convert.py</code> script is provided, which build a unique Docker image for each package, mount the downloaded CEL files as a volume, and then run the gene conversion script <code>R/gene_convert.R</code> inside the image and output the master conversion matrix. Output TSV files live in <code>cels/out/</code>.

<strong>Reproducing</strong>

The entire process can be reproduced by running the following command script from a fresh checkout of this repository. It will take some time:

<pre><code>$ ./generate_matricies_from_scratch.sh
</code></pre>

You can also choose to only build a specific platform, ex.,:

<pre><code>$ ./generate_matricies_from_scratch.sh celegans
</code></pre>

<strong>Identifiers</strong>

Released assets in this repository are availble under the DOI, <code>xyz:1.2.3.4</code>, which can be seen on Zenodo here.

<strong>Related Projects</strong>


	AlexsLemonade/refinebio


<strong>Copyright</strong>

<code>identifier-refinery</code> output assets are released under a CC0 1.0 Universal license. All code is released under the BSD 3-clause license. Input assets are property of the original providers to NCBI GEO, but may be freely downloaded and redistributed unless otherwise noted.

 

https://github.com/AlexsLemonade/identifier-refinery
DOI: 10.5281/zenodo.1322711
title: Identifier Refinery Conversion Matrixes

description: <strong>identifier-refinery</strong>

Tools and assets for easy and reproducable gene identifier conversion.

<strong>Methods</strong>

This repository is used to build matricies which can convert between different gene identifiers.

These conversion matricies are built by:


	Randomly choosing raw CEL files from NCBI GEO for a given platform accession code (in <code>/cels</code>)
	Reading the CEL header and joining Brainarray (e.g., <code>hgu133plus2hsensgprobe</code>) and Bioconductor (e.g., <code>hgu133plus2.db</code>) (x, y) coordinates
	Finding intersecting probe identifiers
	Extracting supported identifiers and probe IDs from the Bioconductor package
	Filtering on probe IDs and Ensembl Gene IDs in Brainarray
	Writing the output to a conversion TSV file
	Check that all output conversion TSV files have a shared SHA1


<strong>Repository Contents</strong>

<strong>Source Files</strong>

The <code>cels</code> directory contains raw CEL files taken from GEO. The list of supported platforms is in <code>supported_microarray_platforms.csv</code>. Source files can be acquired by running the <code>acquire_cels.py</code> script.

<strong>Docker Image</strong>

The conversion scripts are run on custom Docker images.

Two Dockerfiles are provided in this repository - <code>base</code> Docker image, which is used to install the quire R dependancies, and the <code>pd</code> image, which is used to build the required databases for a given platform.

<strong>Conversion Scripts</strong>

A <code>build_and_convert.py</code> script is provided, which build a unique Docker image for each package, mount the downloaded CEL files as a volume, and then run the gene conversion script <code>R/gene_convert.R</code> inside the image and output the master conversion matrix. Output TSV files live in <code>cels/out/</code>.

<strong>Reproducing</strong>

The entire process can be reproduced by running the following command script from a fresh checkout of this repository. It will take some time:

<pre><code>$ ./generate_matricies_from_scratch.sh
</code></pre>

You can also choose to only build a specific platform, ex.,:

<pre><code>$ ./generate_matricies_from_scratch.sh celegans
</code></pre>

<strong>Identifiers</strong>

Released assets in this repository are availble under the DOI, <code>xyz:1.2.3.4</code>, which can be seen on Zenodo here.

<strong>Related Projects</strong>


	AlexsLemonade/refinebio


<strong>Copyright</strong>

<code>identifier-refinery</code> output assets are released under a CC0 1.0 Universal license. All code is released under the BSD 3-clause license. Input assets are property of the original providers to NCBI GEO, but may be freely downloaded and redistributed unless otherwise noted.

 

https://github.com/AlexsLemonade/identifier-refinery
DOI: 10.5517/ccdc.csd.cc2032s0
title: CCDC 1850011: Experimental Crystal Structure Determination

description: Related Article: Masataka Umetani, Takayuki Tanaka, Atsuhiro Osuka|2018|Chemical Science|9|6853|doi:10.1039/C8SC02739K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2032t1
title: CCDC 1850012: Experimental Crystal Structure Determination

description: Related Article: Masataka Umetani, Takayuki Tanaka, Atsuhiro Osuka|2018|Chemical Science|9|6853|doi:10.1039/C8SC02739K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2032v2
title: CCDC 1850013: Experimental Crystal Structure Determination

description: Related Article: Masataka Umetani, Takayuki Tanaka, Atsuhiro Osuka|2018|Chemical Science|9|6853|doi:10.1039/C8SC02739K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc20334d
title: CCDC 1850022: Experimental Crystal Structure Determination

description: Related Article: Masataka Umetani, Takayuki Tanaka, Atsuhiro Osuka|2018|Chemical Science|9|6853|doi:10.1039/C8SC02739K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc20338j
title: CCDC 1850026: Experimental Crystal Structure Determination

description: Related Article: Masataka Umetani, Takayuki Tanaka, Atsuhiro Osuka|2018|Chemical Science|9|6853|doi:10.1039/C8SC02739K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc203c3m
title: CCDC 1850269: Experimental Crystal Structure Determination

description: Related Article: Dongjie Bai, Yao Wang, Minghui He, Xiaoxia Gao, Yabing He|2018|Inorg.Chem.Front.|5|2227|doi:10.1039/C8QI00575C
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc203c4n
title: CCDC 1850270: Experimental Crystal Structure Determination

description: Related Article: Dongjie Bai, Yao Wang, Minghui He, Xiaoxia Gao, Yabing He|2018|Inorg.Chem.Front.|5|2227|doi:10.1039/C8QI00575C
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc203c5p
title: CCDC 1850271: Experimental Crystal Structure Determination

description: Related Article: Dongjie Bai, Yao Wang, Minghui He, Xiaoxia Gao, Yabing He|2018|Inorg.Chem.Front.|5|2227|doi:10.1039/C8QI00575C
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5255/ukda-sn-852887
title: Enemy addiction: Archival documents from 13 United States presidential libraries, 1919-2008
DOI: 10.5517/ccdc.csd.cc1pd3ry
title: CCDC 1560780: Experimental Crystal Structure Determination

description: Related Article: Liming Fan, Yujuan Zhang, Jinfang Liang, Xiaoqing Wang, Hongxiao Lv, Jiang Wang, Li Zhao, Xiutang Zhang|2018|CrystEngComm|20|4752|doi:10.1039/C8CE00877A
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1pq2dw
title: CCDC 1570348: Experimental Crystal Structure Determination

description: Related Article: Liming Fan, Yujuan Zhang, Jinfang Liang, Xiaoqing Wang, Hongxiao Lv, Jiang Wang, Li Zhao, Xiutang Zhang|2018|CrystEngComm|20|4752|doi:10.1039/C8CE00877A
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1pq2fx
title: CCDC 1570349: Experimental Crystal Structure Determination

description: Related Article: Liming Fan, Yujuan Zhang, Jinfang Liang, Xiaoqing Wang, Hongxiao Lv, Jiang Wang, Li Zhao, Xiutang Zhang|2018|CrystEngComm|20|4752|doi:10.1039/C8CE00877A
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.