3,440 Matching Annotations
  1. Aug 2021
    1. Sentinel Common Data ModelExternal Link Disclaimer OHDSI Observational Medical Outcomes Partnership (OMOP) Common Data ModelExternal Link Disclaimer Informatics for Integrating Biology and the Bedside (i2b2)External Link Disclaimer / Accrual to Clinical Trials (ACT) Common Data ModelExternal Link Disclaimer Patient-Centered Outcomes Research Network (PCORnet) Common Data ModelExternal Link Disclaimer United States Core Data for Interoperability (USCDI) Health Level Seven (HL7) Fast Healthcare Interoperability Resources (FHIR)External Link Disclaimer Clinical Data Interchange Standards Consortium (CDISC) Study Data Tabulation Model (SDTM)External Link Disclaimer CDISC SDTM COVID-19 companion guideExternal Link Disclaimer U.S. Department of Veterans Affairs Electronic Health Record (EHR) System National Cancer Institute (NCI) Cancer Data Standards Registry and Repository (caDSR)

      All the clinical data standard links

    1. 4The solution, using the Adapter AnalogySentineli2b2/ACTOMOPPCORNET▪Different countries use different “outlets”.▪There is a need for travel adapters.The Solution: ▪Use a converter between various adapters.▪Allow researchers to ask a question once and receive results from many different sources using a common agreed-upon standard structure, or a Common Data Model.

      Types of various data harmonization formats

    2. Sentinel, PCORnet versions 3.1 and 4.0, OMOP and i2b2/ACT

      Data Harmonization Formats

    3. RWD leveraging Clinical Data Interchange Standards Consortium (CDISC) Study Data Tabulation Model (SDTM) via the FDA Gateway
    1. Rogers, J. P., Watson, C. J., Badenoch, J., Cross, B., Butler, M., Song, J., Hafeez, D., Morrin, H., Rengasamy, E. R., Thomas, L., Ralovska, S., Smakowski, A., Sundaram, R. D., Hunt, C. K., Lim, M. F., Aniwattanapong, D., Singh, V., Hussain, Z., Chakraborty, S., … Rooney, A. G. (2021). Neurology and neuropsychiatry of COVID-19: A systematic review and meta-analysis of the early literature reveals frequent CNS manifestations and key emerging narratives. Journal of Neurology, Neurosurgery & Psychiatry, jnnp-2021-326405. https://doi.org/10.1136/jnnp-2021-326405

    1. Prof. Christina Pagel on Twitter: “THREAD latest on B.1.617.2 variant in England: B.1.617.2 (1st discovered in India) is now dominant in England. Here is a thread summarising latest PHE report and Sanger local data. TLDR: it is NOT good news. 1/7” / Twitter. (n.d.). Retrieved August 24, 2021, from https://twitter.com/chrischirp/status/1399333330286415876

    1. Since it was founded by longtime charity executive Pierre Barnoti as the international offshoot of a Montreal animal welfare charity, SPCAI has spent little more than 20 percent of its total revenue on actual programs and services that help animals.
    1. Youyang Gu on Twitter: “People were worried cases would spike further when the UK lifted almost all remaining restrictions in July. The opposite happened. We must acknowledge that restrictions aren’t all that effective in Western countries. (Except Australia, who just entered their 6th lockdown) https://t.co/l7tygXQqn7” / Twitter. (n.d.). Retrieved August 13, 2021, from https://twitter.com/youyanggu/status/1423415277765734402

    1. Ireland Vaccine Progress. “Dose 1 of 2 Progress ▓▓▓▓▓▓▓▓▓▓░░░░░ 68.5% Fully Vaccinated Progress ▓▓▓▓▓▓▓▓▓░░░░░░ 57.1% As of Wednesday, 14 Jul 2021. Note: Percentages of 16+ Population Only. Data Sources in Bio. #CovidVaccine #COVID19 #COVID19Ireland Https://T.Co/QeiFYM4LcD.” Tweet. @IrelandVaccine (blog), July 15, 2021. https://twitter.com/IrelandVaccine/status/1415688619575103492.

    1. One thing I'd like forward-looking hypertext toolmakers to keep in mind is the ability for the tools to help people answer questions like "What led to legalanthology.ch hosting a copy of this document? Given a URL from one organization, is it possible to look at the graph of internal backlinks (let me focus narrowly on incoming edges originating from the same host)?"

    1. Rafael Irizarry. (2021, August 8). Vaccines work in a gif update: COVID19 cases versus vaccination rates in US states through time. The Delta variant effect can be seen clearly starting in July. States with lower vaccination rates are affected much worse. Https://t.co/e0SQpa8Qg0 [Tweet]. @rafalab. https://twitter.com/rafalab/status/1424440520361787392

  2. Jul 2021
    1. If we had truly robust standards for electronic data interchange and less anxiety about privacy, these kinds of data could be moved around more freely in a structured format. Of course, there are regional exchanges where they do. The data could also be created in structured format to begin with.

      This does exist. Fast Healthcare Interoperability Resources (FHIR; pronounced 'fire') is an open standard that describes data formats and elements (the 'resources' in the name), as well as an application programming interface (API) for exchanging electronic health records.

      See more here: https://hl7.org/fhir/

    1. Alan McNally 💙. (2021, February 5). Our latest lab data for B.1.1.7 prevalence in Pillar 2 samples, as determined by SGTF. Clearly now plateauing at 80-90%. Which to me suggests there are other lineages as transmissible as B.1.1.7......... Https://t.co/toA0GyVsZz [Tweet]. @alanmcn1. https://twitter.com/alanmcn1/status/1357701944027004929

    1. NIHR HPRU in Behavioural Science and Eval Bristol. (2021, May 27). Event: The CONQUEST study has collected data on the contacts, behaviour & symptoms of staff & students @BristolUni during #COVID19 to inform policy & math modelling. Join us for this webinar on 8 June for an update on the study, its impact & future plans. Https://t.co/DHrmferP0L https://t.co/25cOASdyKJ [Tweet]. @HPRU_BSE. https://twitter.com/HPRU_BSE/status/1397906695775473671

    1. Nick Holliman. (2021, May 30). @anthonybmasters @d_spiegel A quick visual summary of data on this week’s article by @anthonybmasters & @d_spiegel The outlook is uncertain, although we have survived a variant once already (B.1.1.7). The data on the effect of variants is analysed as fast as it (reliably) arrives. Https://t.co/vOKmCxYMGT https://t.co/3ZeJJTdRs3 [Tweet]. @binocularity. https://twitter.com/binocularity/status/1398957348492918784

    1. i feel for for tool builders that are serious about building useful software interoperability can actually be a huge 00:45:22 spoon uh to their success um it'll make easier to acquire users it will make it easier to help users embed your own tool in their workflows um you may be also losing some users but 00:45:34 that's okay i guess because it'll create sustainable pressure to you for you to focus on an audience well and build really really useful services for them and if you do that they also won't leave as easily

      I agree. I think companies that allow their users to take their data and run when they want to just create trust. Gone are the days when users automatically thought companies had their best interests at heart, as compared with current-day surveillance capitalists.

    1. The most common impression is that a developer is someone who is a genius and is able to process massive algorithms in their head in a computer-like way to produce code. This is a misguided idea. Developers are just regular people who have invested their time to learn a programming language and to understand the tools, techniques, nuances, and quirks of the technology they are using to produce results. Any professional job, be it a bricklayer, plumber, or indeed a developer, requires you to learn the tools of the trade to build what people need. A developer, by my definition, is simply someone who creates something out of nothing. A property developer takes a piece of land and produces homes for people to live in. A web developer produces apps or websites from nothing.

      How to create a developer mindset

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    1. whereas now, they know that user@domain.com was subscribed to xyz.net at some point and is unsubscribing. Information is gold. Replace user@domain with abcd@senate and xyz.net with warezxxx.net and you've got tabloid gold.
    1. Adam Kucharski on Twitter: “Useful data 👇– quick look suggests odds ratio for detection of B.1.617.2 relative to non-B.1.617.2 in vaccinated group compared to controls is 2.7 (95% CI: 0.7-10) after one dose and 1.2 (0.4-3.6) after two...” / Twitter. (n.d.). Retrieved July 2, 2021, from https://twitter.com/AdamJKucharski/status/1400443351908892675?s=20

  3. Jun 2021
    1. some projects to add to the world of linked data

      I'm so excited to hear an update on this project!

    1. Helen McArdle on Twitter: “The good news: An astonishing 98.2% of over-60s in Scotland are now fully vaccinated. That’s an amazing uptake. It doesn’t mean they are 100% protected of course (and especially not when case rates are high) but their risk of hospitalisation/death is cut by over 90% https://t.co/DzAxkpLvcR” / Twitter. (n.d.). Retrieved June 30, 2021, from https://twitter.com/HMcArdleHT/status/1409821893557768195

    1. But here's the twist. That edit window is wired to your personal cloud. That's where your words land. Then you syndicate your words back to the site you're posting to.

      This is more or less how linked data notifications work. (And Solid, of course, goes beyond that.)

    1. Jeremy Faust MD MS (ER physician) on Twitter: “Number of Covid cases among children in US: >4 million. Number of Covid deaths in US children: 300-400. Number of kids vaccinated: 7 million. Number of kids who died from vaccine-related myocarditis: Zero. #vaccinate @bhrenton @RickABright @angie_rasmussen @celinegounder” / Twitter. (n.d.). Retrieved June 28, 2021, from https://twitter.com/jeremyfaust/status/1408880589319647243?s=20

    1. Michael Makris on Twitter: “The cumulative incidence of VITT after AZ first vaccination in the UK is continuing to increase with the latest data being 1 in 81,000. However this is rather misleading because VITT is age related with a higher incidence in the young. Https://t.co/CSjshAoRsN” / Twitter. (n.d.). Retrieved June 27, 2021, from https://twitter.com/ProfMakris/status/1395457748721184777?s=20

    1. Deepti Gurdasani on Twitter: “I’m still utterly stunned by yesterday’s events—Let me go over this in chronological order & why I’m shocked. - First, in the morning yesterday, we saw a ‘leaked’ report to FT which reported on @PHE_uk data that was not public at the time🧵” / Twitter. (n.d.). Retrieved June 27, 2021, from https://twitter.com/dgurdasani1/status/1396373990986375171

    1. Bolze, A., Cirulli, E. T., Luo, S., White, S., Cassens, T., Jacobs, S., Nguyen, J., Ramirez, J. M., Sandoval, E., Wang, X., Wong, D., Becker, D., Laurent, M., Lu, J. T., Isaksson, M., Washington, N. L., & Lee, W. (2021). Rapid displacement of SARS-CoV-2 variant B.1.1.7 by B.1.617.2 and P.1 in the United States [Preprint]. Infectious Diseases (except HIV/AIDS). https://doi.org/10.1101/2021.06.20.21259195

    1. Woolf, K., McManus, I. C., Martin, C. A., Nellums, L. B., Guyatt, A. L., Melbourne, C., Bryant, L., Gogoi, M., Wobi, F., Al-Oraibi, A., Hassan, O., Gupta, A., John, C., Tobin, M. D., Carr, S., Simpson, S., Gregary, B., Aujayeb, A., Zingwe, S., … Pareek, M. (2021). Ethnic differences in SARS-CoV-2 vaccine hesitancy in United Kingdom healthcare workers: Results from the UK-REACH prospective nationwide cohort study [Preprint]. Public and Global Health. https://doi.org/10.1101/2021.04.26.21255788

    1. To get closer to attaining coveted “rich” metadata and ultimately contribute to a “richer” scholarly communication ecosystem, journals first need to have machine-readable metadata that is clean, consistent, and as interoperable as possible.

      What WordPress plugins provide structured metadata functionality for OpenPhysio.

    1. “The data does not exist independently in the world, nor is it generated spontaneously. Data is constructed by people, from people,” (source 1).
    1. Green and Murphy,Renaissance Rhetoric; Plett,English Renaissance; Middleton,Memory Systems; British Library,Incunabula Short Title Catalogue. Green and Murphy were the primary source. Middleton and Plett, who compiled memorytreatises as a distinct category, allowed me to add extra titles to Green and Murphy’s listings. An Excel file containing the266 early modern treatises graphed here can be emailed upon request.

      Sources of data for this paper. I'd definitely love to get a copy of this Excel file. Might be worth expanding to other languages, countries, and timeperiods as well.

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    1. The US Library of Congress has been designated the official registration authority by the ISO and they publish the entire, official, up-to-date list as a trivial to parse text file for free.
    1. Language Range ... matches ... does not match de de, de-CH, de-AT, de-DE, de-1901, de-AT-1901 en, fr-CH
    2. Because ISO code lists were not always free and because they change over time, a key idea was to create a permanent, stable registry for all of the subtags valid in a language tag.

      Why was it not free???

  4. May 2021
    1. On April 27, 2021, Portugal's data protection authority, the National Data Protection Commission, ordered Statistics Portugal, in carrying out the national census, to suspend processing of personal data in any third country that lacks adequate privacy protections, including the United States

      Cloudflare

    1. The O’Reilly report suggests that the second-most significant barrier to AI adoption is a lack of quality data, with 18% of respondents saying their organization is only beginning to realize the importance of high-quality data.

      Data quality is secondary in the sense that data can be cleaned but generating test data for training AI is a non-starter.

    1. The research found that working 55 hours or more a week was associated with a 35% higher risk of stroke and a 17% higher risk of dying from heart disease, compared with a working week of 35 to 40 hours.
    1. To investigate these hypotheses, I created an election-year-country dataset covering the period from the early 1990s to the present for all post- communist democracies.7 The dataset is structured as a quasi-time series of 93 parliamentary elections in 17 countries from 1991 to 2012, and the depen-dent variable is the natural log of the radical right party’s combined vote share in elections held at time t.

      this is the data, her explanation of the dataset she created

    1. a hypermedia server might use sensors to alert users to the arrival of new material: if a sensor were attached to a document, running a new link to the document would set off the sensor

      Linked data notifications?

      (I like the "sensor" imagery.)

    1. Surely RDF already has something like this...? I tried looking around briefly but couldn't find it.

    1. Draft notes, E-mail, plans, source code, to-do lists, what have you

      The personal nature of this information means that users need control of their information. Tim Berners-Lee's Solid (Social Linked Data) project) looks like it could do some of this stuff.

    1. ReconfigBehSci. (2020, November 18). @danielmabuse yes, we all make mistakes, but a responsible actor also factors the kinds of mistakes she is prone to making into decisions on what actions to take: I’m not that great with my hands, so I never contemplated being a neuro-surgeon. Not everyone should be a public voice on COVID [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1329002783094296577

    1. Robert Colvile. (2021, February 16). The vaccine passports debate is a perfect illustration of my new working theory: That the most important part of modern government, and its most important limitation, is database management. Please stick with me on this—It’s much more interesting than it sounds. (1/?) [Tweet]. @rcolvile. https://twitter.com/rcolvile/status/1361673425140543490

    1. ReconfigBehSci on Twitter: ‘the SciBeh initiative is about bringing knowledge to policy makers and the general public, but I have to say this advert I just came across worries me: Where are the preceding data integrity and data analysis classes? Https://t.co/5LwkC1SVyF’ / Twitter. (n.d.). Retrieved 18 February 2021, from https://twitter.com/SciBeh/status/1362344945697308674

  5. Apr 2021
    1. Mehdi Hasan. (2021, April 12). ‘Given you acknowledged...in March 2020 that Asian countries were masking up at the time, saying we shouldn’t mask up as well was a mistake, wasn’t it... At the time, not just in hindsight?’ My question to Dr Fauci. Listen to his very passionate response: Https://t.co/BAf4qp0m6G [Tweet]. @mehdirhasan. https://twitter.com/mehdirhasan/status/1381405233360814085

    1. Drop missing values from the dataframeIn this method we can see that by using dropmissing() method, we are able to remove the rows having missing values in the data frame. Drop missing values is good for those datasets which are large enough to miss some data that will not affect the prediction and it’s not good for small datasets it may lead to underfitting the models.

      Listwise Deletion

    1. Jeremy Faust MD MS (ER physician) on Twitter: “Let’s talk about the background risk of CVST (cerebral venous sinus thrombosis) versus in those who got J&J vaccine. We are going to focus in on women ages 20-50. We are going to compare the same time period and the same disease (CVST). DEEP DIVE🧵 KEY NUMBERS!” / Twitter. (n.d.). Retrieved April 15, 2021, from https://twitter.com/jeremyfaust/status/1382536833863651330