Merge pull request #18 from arokem/arokem_20240917

More edits based on comments from AJC.

_metadata.yml

@@ -9,12 +9,18 @@ authors:
   - name: Vani Mandava
     affiliation: University of Washington
     roles: writing
-    corresponding: true
     orcid: 0000-0003-3592-9453
   - name: Nicoleta Cristea
     affiliation: University of Washington
     roles: writing
-    corresponding: true
     orcid: 0000-0002-9091-0280
+  - name: Anshul Tambay
+    affiliation: University of Washington
+    roles: writing
+    orcid: 0009-0004-9010-1223
+  - name: Andrew J. Connolly
+    affiliation: University of Washington
+    roles: writing
+    orcid: 0000-0001-5576-8189
 
 bibliography: references.bib

references.bib

@@ -1,3 +1,172 @@
+@MISC{Van-Tuyl2023-vp,
+  title     = "Hiring, managing, and retaining data scientists and Research
+               Software Engineers in academia: A career guidebook from {ADSA}
+               and {US}-{RSE}",
+  author    = "Van Tuyl, Steve (ed )",
+  doi       = {https://doi.org/10.5281/zenodo.8329337},
+  url       = {https://zenodo.org/records/8329337},
+  abstract  = "The importance of data, software, and computation has long been
+               recognized in academia and is reflected in the recent rise of job
+               opportunities for data scientists and research software
+               engineers. Big data, for example, created a wave of novel job
+               descriptions before the term Data Scientist (DS) was widely used.
+               And even though software has become a major driver for research
+               (Nangia and Katz, 2017), Research Software Engineer (RSE) as a
+               formal role has lagged behind in terms of job openings,
+               recognition, and prominence within the community. Despite their
+               importance in the academic research ecosystem, the value of DS
+               and RSE roles is not yet widely understood or appreciated in the
+               academic community, and research data, software, and workflows
+               are, in many domains, still regarded as by-products of research.
+               Data Scientists and Research Software Engineers (DS/RSEs) face
+               similar challenges when it comes to career paths in academia -
+               both are non-traditional academic professions with few incentives
+               and a lack of clear career trajectories. This guidebook presents
+               the challenges and suggestions for solutions to improve the
+               situation and to reach a wide community of stakeholders needed to
+               advance career paths for DS/RSEs.",
+  year      =  2023,
+  keywords  = "data science; research software engineering; career guidebook"
+}
+
+
+@ARTICLE{Adler-Milstein2017-id,
+  title     = "Information blocking: Is it occurring and what policy strategies
+               can address it?",
+  author    = "Adler-Milstein, Julia and Pfeifer, Eric",
+  journal   = "Milbank Q.",
+  publisher = "John Wiley \& Sons, Ltd",
+  volume    =  95,
+  number    =  1,
+  pages     = "117--135",
+  abstract  = "Policy Points: Congress has expressed concern about electronic
+               health record (EHR) vendors and health care providers knowingly
+               interfering with the electronic exchange of patient health
+               informatio...",
+  month     =  mar,
+  year      =  2017,
+  keywords  = "electronic health records; health policy; incentives;
+               interoperability",
+  language  = "en"
+}
+
+@ARTICLE{Barker2024-ox,
+  title     = "A national survey of digital health company experiences with
+               electronic health record application programming interfaces",
+  author    = "Barker, Wesley and Maisel, Natalya and Strawley, Catherine E and
+               Israelit, Grace K and Adler-Milstein, Julia and Rosner, Benjamin",
+  journal   = "J. Am. Med. Inform. Assoc.",
+  publisher = "Oxford Academic",
+  volume    =  31,
+  number    =  4,
+  pages     = "866--874",
+  abstract  = "OBJECTIVES: This study sought to capture current digital health
+               company experiences integrating with electronic health records
+               (EHRs), given new federally regulated standards-based application
+               programming interface (API) policies. MATERIALS AND METHODS: We
+               developed and fielded a survey among companies that develop
+               solutions enabling human interaction with an EHR API. The survey
+               was developed by the University of California San Francisco in
+               collaboration with the Office of the National Coordinator for
+               Health Information Technology, the California Health Care
+               Foundation, and ScaleHealth. The instrument contained questions
+               pertaining to experiences with API integrations, barriers faced
+               during API integrations, and API-relevant policy efforts.
+               RESULTS: About 73\% of companies reported current or previous use
+               of a standards-based EHR API in production. About 57\% of
+               respondents indicated using both standards-based and proprietary
+               APIs to integrate with an EHR, and 24\% worked about equally with
+               both APIs. Most companies reported use of the Fast Healthcare
+               Interoperability Resources standard. Companies reported that
+               standards-based APIs required on average less burden than
+               proprietary APIs to establish and maintain. However, companies
+               face barriers to adopting standards-based APIs, including high
+               fees, lack of realistic clinical testing data, and lack of data
+               elements of interest or value. DISCUSSION: The industry is moving
+               toward the use of standardized APIs to streamline data exchange,
+               with a majority of digital health companies using standards-based
+               APIs to integrate with EHRs. However, barriers persist.
+               CONCLUSION: A large portion of digital health companies use
+               standards-based APIs to interoperate with EHRs. Continuing to
+               improve the resources for digital health companies to find, test,
+               connect, and use these APIs ``without special effort'' will be
+               crucial to ensure future technology robustness and durability.",
+  month     =  apr,
+  year      =  2024,
+  keywords  = "application programming interface; digital health; electronic
+               health record; industry",
+  language  = "en"
+}
+
+@ARTICLE{Gillon2024-vu,
+  title         = "{ODIN}: Open Data In Neurophysiology: Advancements, Solutions
+                   \& Challenges",
+  author        = "Gillon, Colleen J and Baker, Cody and Ly, Ryan and Balzani,
+                   Edoardo and Brunton, Bingni W and Schottdorf, Manuel and
+                   Ghosh, Satrajit and Dehghani, Nima",
+  journal       = "arXiv [q-bio.NC]",
+  abstract      = "Across the life sciences, an ongoing effort over the last 50
+                   years has made data and methods more reproducible and
+                   transparent. This openness has led to transformative insights
+                   and vastly accelerated scientific progress. For example,
+                   structural biology and genomics have undertaken systematic
+                   collection and publication of protein sequences and
+                   structures over the past half-century, and these data have
+                   led to scientific breakthroughs that were unthinkable when
+                   data collection first began. We believe that neuroscience is
+                   poised to follow the same path, and that principles of open
+                   data and open science will transform our understanding of the
+                   nervous system in ways that are impossible to predict at the
+                   moment. To this end, new social structures along with active
+                   and open scientific communities are essential to facilitate
+                   and expand the still limited adoption of open science
+                   practices in our field. Unified by shared values of openness,
+                   we set out to organize a symposium for Open Data in
+                   Neuroscience (ODIN) to strengthen our community and
+                   facilitate transformative neuroscience research at large. In
+                   this report, we share what we learned during this first ODIN
+                   event. We also lay out plans for how to grow this movement,
+                   document emerging conversations, and propose a path toward a
+                   better and more transparent science of tomorrow.",
+  month         =  jul,
+  year          =  2024,
+  archivePrefix = "arXiv",
+  primaryClass  = "q-bio.NC"
+}
+
+@INCOLLECTION{Hermes2023-aw,
+  title     = "How can intracranial {EEG} data be published in a standardized
+               format?",
+  author    = "Hermes, Dora and Cimbalnek, Jan",
+  booktitle = "Studies in Neuroscience, Psychology and Behavioral Economics",
+  publisher = "Springer International Publishing",
+  address   = "Cham",
+  pages     = "595--604",
+  abstract  = "Sharing data or code with publications is not something new and
+               licenses for public sharing have existed since the late 20s
+               century. More recent worldwide efforts have led to an increase in
+               the amount of data shared: funding agencies require that data are
+               shared, journals request that data are made available, and some
+               journals publish papers describing data resources. For
+               intracranial EEG (iEEG) data, considering how and when to share
+               data does not happen only at the stage of publication. Human
+               subjects’ rights demand that data sharing is something that
+               should be considered when writing an ethical protocol and
+               designing a study before data are collected. At that moment, it
+               should already be considered what levels of data will be
+               collected and potentially shared. This includes levels of data
+               directly from the amplifier, reformatted or processed data,
+               clinical information and imaging data. In this chapter we will
+               describe considerations and scholarship behind sharing iEEG data,
+               to make it easier for the iEEG community to share data for
+               reproducibility, teaching, advancing computational efforts,
+               integrating iEEG data with other modalities and allow others to
+               build on previous work.",
+  year      =  2023,
+  language  = "en"
+}
+
+
 @ARTICLE{Hanisch2015-cu,
   title     = "The Virtual Astronomical Observatory: Re-engineering access to
                astronomical data",

sections/01-introduction.qmd

@@ -30,7 +30,7 @@ non-profit organization that was founded in the 1990s developed a set of
 guidelines for licensing of OSS that is designed to protect the rights of
 developers and users. On the technical side, tools such as the Git Source-code
 management system support complex and distributed open-source workflows that
-accelerate, streamline, and robustify OSS development. Governance approaches
+accelerate, streamline, and make OSS development more robust. Governance approaches
 have been honed to address the challenges of managing a range of stakeholder
 interests and to mediate between large numbers of weakly-connected individuals
 that contribute to OSS. When these social and technical innovations are put
@@ -44,9 +44,9 @@ Data and metadata standards that use tools and practices of OSS ("open-source
 standards" henceforth) reap many of the benefits that the OSS model has
 provided in the development of other technologies. The present report explores
 how OSS processes and tools have affected the development of data and metadata
-standards. The report will triangulate common features of a variety of use
-cases; it will identify some of the challenges and pitfalls of this mode of
-standards development, with a particular focus on cross-sector interactions;
-and it will make recommendations for future developments and policies that can
-help this mode of standards development thrive and reach its full potential.
+standards. The report will survey common features of a variety of use cases; it
+will identify some of the challenges and pitfalls of this mode of standards
+development, with a particular focus on cross-sector interactions; and it will
+make recommendations for future developments and policies that can help this
+mode of standards development thrive and reach its full potential.