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CyanOmics: an integrated database of omics for the model cyanobacterium Synechococcus sp. PCC 7002.

Database : the journal of biological databases and curation

Yang Y, Feng J, Li T, Ge F, Zhao J.
PMID: 25632108
Database (Oxford). 2015 Jan 28;2015. doi: 10.1093/database/bau127. Print 2015.

Cyanobacteria are an important group of organisms that carry out oxygenic photosynthesis and play vital roles in both the carbon and nitrogen cycles of the Earth. The annotated genome of Synechococcus sp. PCC 7002, as an ideal model cyanobacterium,...

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Yang Y, Feng J, Li T, et al. CyanOmics: an integrated database of omics for the model cyanobacterium Synechococcus sp. PCC 7002. Database (Oxford). 2015;2015doi: 10.1093/database/bau127.
Yang, Y., Feng, J., Li, T., Ge, F., & Zhao, J. (2015). CyanOmics: an integrated database of omics for the model cyanobacterium Synechococcus sp. PCC 7002. Database : the journal of biological databases and curation, 2015. https://doi.org/10.1093/database/bau127
Yang, Yaohua, et al. "CyanOmics: an integrated database of omics for the model cyanobacterium Synechococcus sp. PCC 7002." Database : the journal of biological databases and curation vol. 2015 (2015). doi: https://doi.org/10.1093/database/bau127
Yang Y, Feng J, Li T, Ge F, Zhao J. CyanOmics: an integrated database of omics for the model cyanobacterium Synechococcus sp. PCC 7002. Database (Oxford). 2015 Jan 28;2015. doi: 10.1093/database/bau127. Print 2015. PMID: 25632108; PMCID: PMC4309022.
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SCovid: single-cell atlases for exposing molecular characteristics of COVID-19 across 10 human tissues.

Nucleic acids research

Qi C, Wang C, Zhao L, Zhu Z, Wang P, Zhang S, Cheng L, Zhang X.
PMID: 34634820
Nucleic Acids Res. 2022 Jan 07;50:D867-D874. doi: 10.1093/nar/gkab881.

SCovid (http://bio-annotation.cn/scovid) aims at providing a comprehensive resource of single-cell data for exposing molecular characteristics of coronavirus disease 2019 (COVID-19) across 10 human tissues. COVID-19, an epidemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been found...

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Qi C, Wang C, Zhao L, et al. SCovid: single-cell atlases for exposing molecular characteristics of COVID-19 across 10 human tissues. Nucleic Acids Res. 2022;50:D867-D874doi: 10.1093/nar/gkab881.
Qi, C., Wang, C., Zhao, L., Zhu, Z., Wang, P., Zhang, S., Cheng, L., & Zhang, X. (2022). SCovid: single-cell atlases for exposing molecular characteristics of COVID-19 across 10 human tissues. Nucleic acids research, 50D867-D874. https://doi.org/10.1093/nar/gkab881
Qi, Changlu, et al. "SCovid: single-cell atlases for exposing molecular characteristics of COVID-19 across 10 human tissues." Nucleic acids research vol. 50 (2022): D867-D874. doi: https://doi.org/10.1093/nar/gkab881
Qi C, Wang C, Zhao L, Zhu Z, Wang P, Zhang S, Cheng L, Zhang X. SCovid: single-cell atlases for exposing molecular characteristics of COVID-19 across 10 human tissues. Nucleic Acids Res. 2022 Jan 07;50:D867-D874. doi: 10.1093/nar/gkab881. PMID: 34634820; PMCID: PMC8524591.
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Shared resources, shared costs--leveraging biocuration resources.

Database : the journal of biological databases and curation

Orchard S, Hermjakob H.
PMID: 25776020
Database (Oxford). 2015 Mar 16;2015. doi: 10.1093/database/bav009. Print 2015.

The manual curation of the information in biomedical resources is an expensive task. This article argues the value of this approach in comparison with other apparently less costly options, such as automated annotation or text-mining, then discusses ways in...

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Orchard S, Hermjakob H. Shared resources, shared costs--leveraging biocuration resources. Database (Oxford). 2015;2015doi: 10.1093/database/bav009.
Orchard, S., & Hermjakob, H. (2015). Shared resources, shared costs--leveraging biocuration resources. Database : the journal of biological databases and curation, 2015. https://doi.org/10.1093/database/bav009
Orchard, Sandra, and Hermjakob, Henning. "Shared resources, shared costs--leveraging biocuration resources." Database : the journal of biological databases and curation vol. 2015 (2015). doi: https://doi.org/10.1093/database/bav009
Orchard S, Hermjakob H. Shared resources, shared costs--leveraging biocuration resources. Database (Oxford). 2015 Mar 16;2015. doi: 10.1093/database/bav009. Print 2015. PMID: 25776020; PMCID: PMC4360620.
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LMPID: a manually curated database of linear motifs mediating protein-protein interactions.

Database : the journal of biological databases and curation

Sarkar D, Jana T, Saha S.
PMID: 25776024
Database (Oxford). 2015 Mar 16;2015. doi: 10.1093/database/bav014. Print 2015.

Linear motifs (LMs), used by a subset of all protein-protein interactions (PPIs), bind to globular receptors or domains and play an important role in signaling networks. LMPID (Linear Motif mediated Protein Interaction Database) is a manually curated database which...

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Sarkar D, Jana T, Saha S. LMPID: a manually curated database of linear motifs mediating protein-protein interactions. Database (Oxford). 2015;2015doi: 10.1093/database/bav014.
Sarkar, D., Jana, T., & Saha, S. (2015). LMPID: a manually curated database of linear motifs mediating protein-protein interactions. Database : the journal of biological databases and curation, 2015. https://doi.org/10.1093/database/bav014
Sarkar, Debasree, et al. "LMPID: a manually curated database of linear motifs mediating protein-protein interactions." Database : the journal of biological databases and curation vol. 2015 (2015). doi: https://doi.org/10.1093/database/bav014
Sarkar D, Jana T, Saha S. LMPID: a manually curated database of linear motifs mediating protein-protein interactions. Database (Oxford). 2015 Mar 16;2015. doi: 10.1093/database/bav014. Print 2015. PMID: 25776024; PMCID: PMC4360622.
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Enhancing studies of the connectome in autism using the autism brain imaging data exchange II.

Scientific data

Di Martino A, O'Connor D, Chen B, Alaerts K, Anderson JS, Assaf M, Balsters JH, Baxter L, Beggiato A, Bernaerts S, Blanken LM, Bookheimer SY, Braden BB, Byrge L, Castellanos FX, Dapretto M, Delorme R, Fair DA, Fishman I, Fitzgerald J, Gallagher L, Keehn RJ, Kennedy DP, Lainhart JE, Luna B, Mostofsky SH, Müller RA, Nebel MB, Nigg JT, O'Hearn K, Solomon M, Toro R, Vaidya CJ, Wenderoth N, White T, Craddock RC, Lord C, Leventhal B, Milham MP.
PMID: 28291247
Sci Data. 2017 Mar 14;4:170010. doi: 10.1038/sdata.2017.10.

The second iteration of the Autism Brain Imaging Data Exchange (ABIDE II) aims to enhance the scope of brain connectomics research in Autism Spectrum Disorder (ASD). Consistent with the initial ABIDE effort (ABIDE I), that released 1112 datasets in...

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Di Martino A, O'Connor D, Chen B, et al. Enhancing studies of the connectome in autism using the autism brain imaging data exchange II. Sci Data. 2017;4:170010doi: 10.1038/sdata.2017.10.
Di Martino, A., O'Connor, D., Chen, B., Alaerts, K., Anderson, J. S., Assaf, M., Balsters, J. H., Baxter, L., Beggiato, A., Bernaerts, S., Blanken, L. M., Bookheimer, S. Y., Braden, B. B., Byrge, L., Castellanos, F. X., Dapretto, M., Delorme, R., Fair, D. A., Fishman, I., Fitzgerald, J., Gallagher, L., Keehn, R. J., Kennedy, D. P., Lainhart, J. E., Luna, B., Mostofsky, S. H., Müller, R. A., Nebel, M. B., Nigg, J. T., O'Hearn, K., Solomon, M., Toro, R., Vaidya, C. J., Wenderoth, N., White, T., Craddock, R. C., Lord, C., Leventhal, B., & Milham, M. P. (2017). Enhancing studies of the connectome in autism using the autism brain imaging data exchange II. Scientific data, 4170010. https://doi.org/10.1038/sdata.2017.10
Di Martino, Adriana, et al. "Enhancing studies of the connectome in autism using the autism brain imaging data exchange II." Scientific data vol. 4 (2017): 170010. doi: https://doi.org/10.1038/sdata.2017.10
Di Martino A, O'Connor D, Chen B, Alaerts K, Anderson JS, Assaf M, Balsters JH, Baxter L, Beggiato A, Bernaerts S, Blanken LM, Bookheimer SY, Braden BB, Byrge L, Castellanos FX, Dapretto M, Delorme R, Fair DA, Fishman I, Fitzgerald J, Gallagher L, Keehn RJ, Kennedy DP, Lainhart JE, Luna B, Mostofsky SH, Müller RA, Nebel MB, Nigg JT, O'Hearn K, Solomon M, Toro R, Vaidya CJ, Wenderoth N, White T, Craddock RC, Lord C, Leventhal B, Milham MP. Enhancing studies of the connectome in autism using the autism brain imaging data exchange II. Sci Data. 2017 Mar 14;4:170010. doi: 10.1038/sdata.2017.10. PMID: 28291247; PMCID: PMC5349246.
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The climate hazards infrared precipitation with stations--a new environmental record for monitoring extremes.

Scientific data

Funk C, Peterson P, Landsfeld M, Pedreros D, Verdin J, Shukla S, Husak G, Rowland J, Harrison L, Hoell A, Michaelsen J.
PMID: 26646728
Sci Data. 2015 Dec 08;2:150066. doi: 10.1038/sdata.2015.66.

The Climate Hazards group Infrared Precipitation with Stations (CHIRPS) dataset builds on previous approaches to 'smart' interpolation techniques and high resolution, long period of record precipitation estimates based on infrared Cold Cloud Duration (CCD) observations. The algorithm i) is...

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Funk C, Peterson P, Landsfeld M, et al. The climate hazards infrared precipitation with stations--a new environmental record for monitoring extremes. Sci Data. 2015;2:150066doi: 10.1038/sdata.2015.66.
Funk, C., Peterson, P., Landsfeld, M., Pedreros, D., Verdin, J., Shukla, S., Husak, G., Rowland, J., Harrison, L., Hoell, A., & Michaelsen, J. (2015). The climate hazards infrared precipitation with stations--a new environmental record for monitoring extremes. Scientific data, 2150066. https://doi.org/10.1038/sdata.2015.66
Funk, Chris, et al. "The climate hazards infrared precipitation with stations--a new environmental record for monitoring extremes." Scientific data vol. 2 (2015): 150066. doi: https://doi.org/10.1038/sdata.2015.66
Funk C, Peterson P, Landsfeld M, Pedreros D, Verdin J, Shukla S, Husak G, Rowland J, Harrison L, Hoell A, Michaelsen J. The climate hazards infrared precipitation with stations--a new environmental record for monitoring extremes. Sci Data. 2015 Dec 08;2:150066. doi: 10.1038/sdata.2015.66. PMID: 26646728; PMCID: PMC4672685.
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Developing a dataset to track aid for reproductive, maternal, newborn and child health, 2003-2013.

Scientific data

Grollman C, Arregoces L, Martinez-Alvarez M, Pitt C, Powell-Jackson T, Hsu J, Greco G, Borghi J.
PMID: 28350378
Sci Data. 2017 Mar 28;4:170038. doi: 10.1038/sdata.2017.38.

We created a dataset to generate estimates of donor-reported 'official development assistance' and private grants (ODA+) to reproductive, maternal, newborn and child health (RMNCH) by donor, recipient country and activity type over the period 2003-2013. We collected disbursement information...

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Grollman C, Arregoces L, Martinez-Alvarez M, et al. Developing a dataset to track aid for reproductive, maternal, newborn and child health, 2003-2013. Sci Data. 2017;4:170038doi: 10.1038/sdata.2017.38.
Grollman, C., Arregoces, L., Martinez-Alvarez, M., Pitt, C., Powell-Jackson, T., Hsu, J., Greco, G., & Borghi, J. (2017). Developing a dataset to track aid for reproductive, maternal, newborn and child health, 2003-2013. Scientific data, 4170038. https://doi.org/10.1038/sdata.2017.38
Grollman, Christopher, et al. "Developing a dataset to track aid for reproductive, maternal, newborn and child health, 2003-2013." Scientific data vol. 4 (2017): 170038. doi: https://doi.org/10.1038/sdata.2017.38
Grollman C, Arregoces L, Martinez-Alvarez M, Pitt C, Powell-Jackson T, Hsu J, Greco G, Borghi J. Developing a dataset to track aid for reproductive, maternal, newborn and child health, 2003-2013. Sci Data. 2017 Mar 28;4:170038. doi: 10.1038/sdata.2017.38. PMID: 28350378; PMCID: PMC5369316.
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A reference set of curated biomedical data and metadata from clinical case reports.

Scientific data

Caufield JH, Zhou Y, Garlid AO, Setty SP, Liem DA, Cao Q, Lee JM, Murali S, Spendlove S, Wang W, Zhang L, Sun Y, Bui A, Hermjakob H, Watson KE, Ping P.
PMID: 30457569
Sci Data. 2018 Nov 20;5:180258. doi: 10.1038/sdata.2018.258.

Clinical case reports (CCRs) provide an important means of sharing clinical experiences about atypical disease phenotypes and new therapies. However, published case reports contain largely unstructured and heterogeneous clinical data, posing a challenge to mining relevant information. Current indexing...

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Caufield JH, Zhou Y, Garlid AO, et al. A reference set of curated biomedical data and metadata from clinical case reports. Sci Data. 2018;5:180258doi: 10.1038/sdata.2018.258.
Caufield, J. H., Zhou, Y., Garlid, A. O., Setty, S. P., Liem, D. A., Cao, Q., Lee, J. M., Murali, S., Spendlove, S., Wang, W., Zhang, L., Sun, Y., Bui, A., Hermjakob, H., Watson, K. E., & Ping, P. (2018). A reference set of curated biomedical data and metadata from clinical case reports. Scientific data, 5180258. https://doi.org/10.1038/sdata.2018.258
Caufield, J Harry, et al. "A reference set of curated biomedical data and metadata from clinical case reports." Scientific data vol. 5 (2018): 180258. doi: https://doi.org/10.1038/sdata.2018.258
Caufield JH, Zhou Y, Garlid AO, Setty SP, Liem DA, Cao Q, Lee JM, Murali S, Spendlove S, Wang W, Zhang L, Sun Y, Bui A, Hermjakob H, Watson KE, Ping P. A reference set of curated biomedical data and metadata from clinical case reports. Sci Data. 2018 Nov 20;5:180258. doi: 10.1038/sdata.2018.258. PMID: 30457569; PMCID: PMC6244181.
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Building a PubMed knowledge graph.

Scientific data

Xu J, Kim S, Song M, Jeong M, Kim D, Kang J, Rousseau JF, Li X, Xu W, Torvik VI, Bu Y, Chen C, Ebeid IA, Li D, Ding Y.
PMID: 32591513
Sci Data. 2020 Jun 26;7(1):205. doi: 10.1038/s41597-020-0543-2.

PubMed

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Xu J, Kim S, Song M, et al. Building a PubMed knowledge graph. Sci Data. 2020;7(1):205doi: 10.1038/s41597-020-0543-2.
Xu, J., Kim, S., Song, M., Jeong, M., Kim, D., Kang, J., Rousseau, J. F., Li, X., Xu, W., Torvik, V. I., Bu, Y., Chen, C., Ebeid, I. A., Li, D., & Ding, Y. (2020). Building a PubMed knowledge graph. Scientific data, 7(1), 205. https://doi.org/10.1038/s41597-020-0543-2
Xu, Jian, et al. "Building a PubMed knowledge graph." Scientific data vol. 7,1 (2020): 205. doi: https://doi.org/10.1038/s41597-020-0543-2
Xu J, Kim S, Song M, Jeong M, Kim D, Kang J, Rousseau JF, Li X, Xu W, Torvik VI, Bu Y, Chen C, Ebeid IA, Li D, Ding Y. Building a PubMed knowledge graph. Sci Data. 2020 Jun 26;7(1):205. doi: 10.1038/s41597-020-0543-2. PMID: 32591513; PMCID: PMC7320186.
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EpiDBase: a manually curated database for small molecule modulators of epigenetic landscape.

Database : the journal of biological databases and curation

Loharch S, Bhutani I, Jain K, Gupta P, Sahoo DK, Parkesh R.
PMID: 25776023
Database (Oxford). 2015 Mar 16;2015. doi: 10.1093/database/bav013. Print 2015.

We have developed EpiDBase (www.epidbase.org), an interactive database of small molecule ligands of epigenetic protein families by bringing together experimental, structural and chemoinformatic data in one place. Currently, EpiDBase encompasses 5784 unique ligands (11 422 entries) of various epigenetic...

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Loharch S, Bhutani I, Jain K, et al. EpiDBase: a manually curated database for small molecule modulators of epigenetic landscape. Database (Oxford). 2015;2015doi: 10.1093/database/bav013.
Loharch, S., Bhutani, I., Jain, K., Gupta, P., Sahoo, D. K., & Parkesh, R. (2015). EpiDBase: a manually curated database for small molecule modulators of epigenetic landscape. Database : the journal of biological databases and curation, 2015. https://doi.org/10.1093/database/bav013
Loharch, Saurabh, et al. "EpiDBase: a manually curated database for small molecule modulators of epigenetic landscape." Database : the journal of biological databases and curation vol. 2015 (2015). doi: https://doi.org/10.1093/database/bav013
Loharch S, Bhutani I, Jain K, Gupta P, Sahoo DK, Parkesh R. EpiDBase: a manually curated database for small molecule modulators of epigenetic landscape. Database (Oxford). 2015 Mar 16;2015. doi: 10.1093/database/bav013. Print 2015. PMID: 25776023; PMCID: PMC4360624.
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MIMIC-III, a freely accessible critical care database.

Scientific data

Johnson AE, Pollard TJ, Shen L, Lehman LW, Feng M, Ghassemi M, Moody B, Szolovits P, Celi LA, Mark RG.
PMID: 27219127
Sci Data. 2016 May 24;3:160035. doi: 10.1038/sdata.2016.35.

MIMIC-III ('Medical Information Mart for Intensive Care') is a large, single-center database comprising information relating to patients admitted to critical care units at a large tertiary care hospital. Data includes vital signs, medications, laboratory measurements, observations and notes charted...

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Johnson AE, Pollard TJ, Shen L, et al. MIMIC-III, a freely accessible critical care database. Sci Data. 2016;3:160035doi: 10.1038/sdata.2016.35.
Johnson, A. E., Pollard, T. J., Shen, L., Lehman, L. W., Feng, M., Ghassemi, M., Moody, B., Szolovits, P., Celi, L. A., & Mark, R. G. (2016). MIMIC-III, a freely accessible critical care database. Scientific data, 3160035. https://doi.org/10.1038/sdata.2016.35
Johnson, Alistair E W, et al. "MIMIC-III, a freely accessible critical care database." Scientific data vol. 3 (2016): 160035. doi: https://doi.org/10.1038/sdata.2016.35
Johnson AE, Pollard TJ, Shen L, Lehman LW, Feng M, Ghassemi M, Moody B, Szolovits P, Celi LA, Mark RG. MIMIC-III, a freely accessible critical care database. Sci Data. 2016 May 24;3:160035. doi: 10.1038/sdata.2016.35. PMID: 27219127; PMCID: PMC4878278.
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Imaging and clinical data archive for head and neck squamous cell carcinoma patients treated with radiotherapy.

Scientific data

Grossberg AJ, Mohamed ASR, Elhalawani H, Bennett WC, Smith KE, Nolan TS, Williams B, Chamchod S, Heukelom J, Kantor ME, Browne T, Hutcheson KA, Gunn GB, Garden AS, Morrison WH, Frank SJ, Rosenthal DI, Freymann JB, Fuller CD.
PMID: 30179230
Sci Data. 2018 Sep 04;5:180173. doi: 10.1038/sdata.2018.173.

Cross sectional imaging is essential for the patient-specific planning and delivery of radiotherapy, a primary determinant of head and neck cancer outcomes. Due to challenges ensuring data quality and patient de-identification, publicly available datasets including diagnostic and radiation treatment...

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Grossberg AJ, Mohamed ASR, Elhalawani H, et al. Imaging and clinical data archive for head and neck squamous cell carcinoma patients treated with radiotherapy. Sci Data. 2018;5:180173doi: 10.1038/sdata.2018.173.
Grossberg, A. J., Mohamed, A. S. R., Elhalawani, H., Bennett, W. C., Smith, K. E., Nolan, T. S., Williams, B., Chamchod, S., Heukelom, J., Kantor, M. E., Browne, T., Hutcheson, K. A., Gunn, G. B., Garden, A. S., Morrison, W. H., Frank, S. J., Rosenthal, D. I., Freymann, J. B., & Fuller, C. D. (2018). Imaging and clinical data archive for head and neck squamous cell carcinoma patients treated with radiotherapy. Scientific data, 5180173. https://doi.org/10.1038/sdata.2018.173
Grossberg, Aaron J, et al. "Imaging and clinical data archive for head and neck squamous cell carcinoma patients treated with radiotherapy." Scientific data vol. 5 (2018): 180173. doi: https://doi.org/10.1038/sdata.2018.173
Grossberg AJ, Mohamed ASR, Elhalawani H, Bennett WC, Smith KE, Nolan TS, Williams B, Chamchod S, Heukelom J, Kantor ME, Browne T, Hutcheson KA, Gunn GB, Garden AS, Morrison WH, Frank SJ, Rosenthal DI, Freymann JB, Fuller CD. Imaging and clinical data archive for head and neck squamous cell carcinoma patients treated with radiotherapy. Sci Data. 2018 Sep 04;5:180173. doi: 10.1038/sdata.2018.173. PMID: 30179230; PMCID: PMC6190723.
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Showing 37 to 48 of 50 entries