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Showing 37 to 48 of 50 entries
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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,...

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 ( 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...

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...

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...

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...

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...

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...

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...

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.


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 (, 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...

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...

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...

Showing 37 to 48 of 50 entries