Reviewer name and names of any other individual's who aided in reviewer	Chris Armit
Do you understand and agree to our policy of having open and named reviews, and having your review included with the published manuscript. (If no, please inform the editor that you cannot review this manuscript.)	Yes
Is the language of sufficient quality?	Yes
Please add additional comments on language quality to clarify if needed	A minor point is that the contents of the Restricted Access AmsterdamUMCdb tabular data files are in Dutch, and so researchers may have to familiarise themselves with some of the terms that are used in the data files e.g. Neurochirurgie = Neurosurgery, Vaatchirurgie = Vascular Surgery, Verloskunde = Midwifery etc.
Is there a clear statement of need explaining what problems the software is designed to solve and who the target audience is?	Yes
Additional Comments	This Technical Release manuscript describes Sepsis-3 criteria in AmsterdamUMCdb. Sepsis-3 is the third consensus definition of sepsis, which includes a revised definition of sepsis based on a scoring system that utilises Sequential Organ Failure Assessment (SOFA). SOFA measures the severity of organ dysfunction across six domains including respiratory, neurological, cardiovascular, liver, coagulation and renal systems. AmsterdamUMCdb is a freely accessible intensive care database with de-identified health data relating to intensive care unit admissions, and includes demographics, vital signs, laboratory tests and medications.
Is the source code available, and has an appropriate Open Source Initiative license <a href="https://opensource.org/licenses" target="_blank">(https://opensource.org/licenses)</a> been assigned to the code?	Yes
Additional Comments	The manuscript is well written, and the software is publicly available from GitHub (https://github.com/tedinburgh/sepsis3-amsterdamumcdb), where it has been ascribed an OSI-approved MIT license.
As Open Source Software are there guidelines on how to contribute, report issues or seek support on the code?	Yes
Additional Comments	The GitHub archive was created by Dr Tom Edinburgh, who is the contact author for this manuscript.
Is the code executable?	Yes
Additional Comments
Is installation/deployment sufficiently outlined in the paper and documentation, and does it proceed as outlined?	Yes
Additional Comments
Is the documentation provided clear and user friendly?	Yes
Additional Comments	The AmsterdamUMCdb Test Data is Restricted Access. I outline below the various steps that were needed to access the Test Data. • To gain access to AmsterdamUMCdb, one must first complete the Data or Specimens Only Research (DSOR) course from CITI • Reviewers must then submit a signed copy of application form arfeula_v1.6.pdf • This application form and the link to the DSOR course are available from the following link: • https://www.amsterdammedicaldatascience.nl/#amsterdamumcdb • This application must be counter-signed by an intensivist i.e. a health professional who specialises in the care of critically ill patients, and who is the named reference on the application from Once the application form has been approved, reviewers must do the following: • Create an account on EASY using the same institutional e-mail address as on their form • Complete their user profile in EASY, including organisation and department • Request download permission for the dataset on EASY Once registered with EASY, reviewers will be granted access to the AmsterdamUMCdb Data File that is archived in EASY: • https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:130980 There is currently a single file archived on this link. This single file is a PDF file that states the following: • Your request has been granted, the dataset has been archived outside EASY due to the size. • Please contact DANS at info@dans.knaw.nl for delivery of the dataset to you. Preferably mention the citation of the dataset: • Elbers, Dr. P.W.G. (Amsterdam UMC) (2019): AmsterdamUMCdb v1.0.2. DANS. https://doi.org/10.17026/dans-22u-f8vd Reviewers should then contact DANS (Data Archiving and Networked Services), who should send a SURFfilesender link to the 8.3GB AmsterdamUMCdb-v1.0.2.zip archive. This link is active for 3 weeks. The zip file contains seven tabular data files (CSV file format) that I list below. • admissions.csv • drugitems.csv • freetextitems.csv • listitems.csv • numericitems.csv • procedureorderitems.csv • processitems.csv
Is there a clearly-stated list of dependencies, and is the core functionality of the software documented to a satisfactory level?	Yes
Additional Comments
Have any claims of performance been sufficiently tested and compared to other commonly-used packages?	Not applicable
Additional Comments
Are there (ideally real world) examples demonstrating use of the software?	Yes
Additional Comments
Is automated testing used or are there manual steps described so that the functionality of the software can be verified?	Yes
Additional Comments
Any Additional Overall Comments to the Author	This Technical Release manuscript describes Sepsis-3 criteria in AmsterdamUMCdb. Sepsis-3 is the third consensus definition of sepsis, which includes a revised definition of sepsis based on a scoring system that utilises Sequential Organ Failure Assessment (SOFA). SOFA measures the severity of organ dysfunction across six domains including respiratory, neurological, cardiovascular, liver, coagulation and renal systems. AmsterdamUMCdb is a freely accessible intensive care database with de-identified health data relating to intensive care unit admissions, and includes demographics, vital signs, laboratory tests and medications. The manuscript is well written, and the software is publicly available from GitHub (https://github.com/tedinburgh/sepsis3-amsterdamumcdb), where it has been ascribed an OSI-approved MIT license. The AmsterdamUMCdb Test Data is Restricted Access. I am grateful to the authors for providing me with access to this very significant data resource. I outline below the various steps that were needed to access the Test Data. • To gain access to AmsterdamUMCdb, one must first complete the Data or Specimens Only Research (DSOR) course from CITI • Reviewers must then submit a signed copy of application form arfeula_v1.6.pdf • This application form and the link to the DSOR course are available from the following link: • https://www.amsterdammedicaldatascience.nl/#amsterdamumcdb • This application must be counter-signed by an intensivist i.e. a health professional who specialises in the care of critically ill patients, and who is the named reference on the application from Once the application form has been approved, reviewers must do the following: • Create an account on EASY using the same institutional e-mail address as on their form • Complete their user profile in EASY, including organisation and department • Request download permission for the dataset on EASY Once registered with EASY, reviewers will be granted access to the AmsterdamUMCdb Data File that is archived in EASY: • https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:130980 There is currently a single file archived on this link. This single file is a PDF file that states the following: • Your request has been granted, the dataset has been archived outside EASY due to the size. • Please contact DANS at info@dans.knaw.nl for delivery of the dataset to you. Preferably mention the citation of the dataset: • Elbers, Dr. P.W.G. (Amsterdam UMC) (2019): AmsterdamUMCdb v1.0.2. DANS. https://doi.org/10.17026/dans-22u-f8vd Reviewers should then contact DANS (Data Archiving and Networked Services), who should send a SURFfilesender link to the 8.3GB AmsterdamUMCdb-v1.0.2.zip archive. This link is active for 3 weeks. The zip file contains seven tabular data files (CSV file format) that I list below. • admissions.csv • drugitems.csv • freetextitems.csv • listitems.csv • numericitems.csv • procedureorderitems.csv • processitems.csv A minor point is that the contents of the tabular data files are in Dutch, and so researchers may have to familiarise themselves with some of the terms that are used in the data files e.g. Neurochirurgie = Neurosurgery, Vaatchirurgie = Vascular Surgery, Verloskunde = Midwifery etc. I was wondering whether it would it be possible to streamline the application process for AmsterdamUMCdb? For example, as the AmsterdamUMCdb dataset is archived outside of EASY, is it necessary to register with EASY? It may be swifter for a researcher if this step was omitted and they were invited to contact DANS at an earlier step in the process.
Recommendation	Accept