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13 | 13 |
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14 | | -<title>gaia-intro.knit</title> |
| 14 | +<title> OHDSI GIS WG</title> |
15 | 15 |
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16 | | -<script src="site_libs/header-attrs-2.25/header-attrs.js"></script> |
| 16 | +<script src="site_libs/header-attrs-2.28/header-attrs.js"></script> |
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335 | 335 | Home |
336 | 336 | </a> |
337 | 337 | </li> |
| 338 | +<li> |
| 339 | + <a href="getting-started.html"> |
| 340 | + <span class="fa fa-home"></span> |
| 341 | + |
| 342 | + Getting Started |
| 343 | + </a> |
| 344 | +</li> |
338 | 345 | <li class="dropdown"> |
339 | 346 | <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> |
340 | 347 | <span class="fa fa-earth"></span> |
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350 | 357 | <li> |
351 | 358 | <a href="gaia-principles.html">Design</a> |
352 | 359 | </li> |
353 | | - <li class="dropdown-submenu"> |
354 | | - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">Specifications</a> |
355 | | - <ul class="dropdown-menu" role="menu"> |
356 | | - <li> |
357 | | - <a href="gaia-terminology.html">Terminology</a> |
358 | | - </li> |
359 | | - <li> |
360 | | - <a href="gaia-datamodels.html">Data Models</a> |
361 | | - </li> |
362 | | - </ul> |
363 | | - </li> |
364 | | - </ul> |
365 | | -</li> |
366 | | -<li class="dropdown"> |
367 | | - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> |
368 | | - <span class="fa fa-cubes"></span> |
369 | | - |
370 | | - Gaia Framework |
371 | | - |
372 | | - <span class="caret"></span> |
373 | | - </a> |
374 | | - <ul class="dropdown-menu" role="menu"> |
375 | 360 | <li> |
376 | | - <a href="fw-overview.html">Overview</a> |
| 361 | + <a href="schema-extensions.html">Schema Extensions</a> |
377 | 362 | </li> |
378 | 363 | <li> |
379 | | - <a href="fw-gaia-catalog.html">Gaia Catalog</a> |
| 364 | + <a href="gaiaDB.html">gaiaDB</a> |
380 | 365 | </li> |
381 | 366 | <li> |
382 | | - <a href="fw-gaia-core.html">Gaia Core</a> |
| 367 | + <a href="gaiaCore.html">gaiaCore</a> |
383 | 368 | </li> |
384 | | - <li class="dropdown-submenu"> |
385 | | - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">Extensions</a> |
386 | | - <ul class="dropdown-menu" role="menu"> |
387 | | - <li> |
388 | | - <a href="fw-gaia-extensions.html">Overview</a> |
389 | | - </li> |
390 | | - <li> |
391 | | - <a href="fw-gaia-extensions-ohdsi.html">GaiaOhdsi</a> |
392 | | - </li> |
393 | | - </ul> |
| 369 | + <li> |
| 370 | + <a href="gaiaOHDSI.html">gaiaOHDSI</a> |
394 | 371 | </li> |
395 | 372 | </ul> |
396 | 373 | </li> |
397 | | -<li class="dropdown"> |
398 | | - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> |
| 374 | +<li> |
| 375 | + <a href="how-to.html"> |
399 | 376 | <span class="fa fa-question"></span> |
400 | 377 |
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401 | 378 | How to |
402 | | - |
403 | | - <span class="caret"></span> |
404 | 379 | </a> |
405 | | - <ul class="dropdown-menu" role="menu"> |
406 | | - <li> |
407 | | - <a href="ht-get-started.html">Get Started with Gaia</a> |
408 | | - </li> |
409 | | - <li> |
410 | | - <a href="ht-local-dataset.html">Use a Local Dataset</a> |
411 | | - </li> |
412 | | - <li> |
413 | | - <a href="ht-geocode.html">Geocode for OMOP Database Addresses</a> |
414 | | - </li> |
415 | | - <li> |
416 | | - <a href="geocodingCohort.html">Geocode an OMOP Cohort</a> |
417 | | - </li> |
418 | | - <li> |
419 | | - <a href="ht-add-data-source.html">Add Data Sources to a Local gaiaDB Instance</a> |
420 | | - </li> |
421 | | - <li> |
422 | | - <a href="ht-share-data-source.html">Share Your Local Data Sources</a> |
423 | | - </li> |
424 | | - </ul> |
425 | 380 | </li> |
426 | | -<li class="dropdown"> |
427 | | - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> |
| 381 | +<li> |
| 382 | + <a href="getting-involved.html"> |
428 | 383 | <span class="fa fa-info"></span> |
429 | 384 |
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430 | 385 | Getting Involved |
431 | | - |
432 | | - <span class="caret"></span> |
433 | 386 | </a> |
434 | | - <ul class="dropdown-menu" role="menu"> |
435 | | - <li> |
436 | | - <a href="gi-propose-usecase.html">Use Case Proposals</a> |
437 | | - </li> |
438 | | - <li> |
439 | | - <a href="gi-edit-docs.html">How to Edit Documentation</a> |
440 | | - </li> |
441 | | - </ul> |
442 | 387 | </li> |
443 | 388 | </ul> |
444 | 389 | <ul class="nav navbar-nav navbar-right"> |
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457 | 402 |
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458 | 403 |
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459 | 404 |
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460 | | -<h1 class="title toc-ignore"><div> |
461 | | -<img src="ohdsi40x40.png"></img> OHDSI GIS WG |
462 | | -</div></h1> |
| 405 | +<h1 class="title toc-ignore"><img src="ohdsi40x40.png"></img> OHDSI GIS |
| 406 | +WG</h1> |
463 | 407 |
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464 | 408 | </div> |
465 | 409 |
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@@ -601,6 +545,71 @@ <h3>Federated networks and research</h3> |
601 | 545 | </div> |
602 | 546 | </div> |
603 | 547 | </div> |
| 548 | +<div id="added-from-gaia-framework-overview-below" |
| 549 | +class="section level1"> |
| 550 | +<h1>Added from Gaia Framework Overview (below)</h1> |
| 551 | +</div> |
| 552 | +<div id="gaia-framework-overview" class="section level1"> |
| 553 | +<h1><strong>Gaia Framework Overview</strong></h1> |
| 554 | +<div> |
| 555 | +<img src="images/framework_overview.png"></img> |
| 556 | +</div> |
| 557 | +<p>The Gaia Framework provides the highest-level view of the components |
| 558 | +that compose Gaia; the framework is divided into three main parts, a |
| 559 | +functional metadata repository (Catalog), staging database and execution |
| 560 | +engine (Core), and ecosystem of Gaia-compatible software packages |
| 561 | +(Extensions):</p> |
| 562 | +<hr /> |
| 563 | +<p><br></p> |
| 564 | +<div id="gaia-catalog" class="section level2"> |
| 565 | +<h2><a href="gaia-catalog.html">Gaia Catalog</a></h2> |
| 566 | +<p>A readily-extensible catalog of source datasets. Gaia Catalog |
| 567 | +contains metadata for public geospatial datasets. Descriptive metadata |
| 568 | +facilitates search and discovery of relevant datasets. Functional |
| 569 | +metadata (machine-actionable instructions) enables automated retrieval, |
| 570 | +extraction, transformation, and loading of public datasets and their |
| 571 | +constituent variables.</p> |
| 572 | +<hr /> |
| 573 | +<p><br></p> |
| 574 | +</div> |
| 575 | +<div id="gaia-core" class="section level2"> |
| 576 | +<h2><a href="gaia-core.html">Gaia Core</a></h2> |
| 577 | +<p>Gaia Core is the central functionality and storage of Gaia and itself |
| 578 | +consists of two main features: a <strong>staging database</strong> and |
| 579 | +an <strong>execution engine</strong>.</p> |
| 580 | +<p>The staging database is a PostGIS database with a replica copy of the |
| 581 | +Gaia Catalog installed in a schema named “backbone”. In this database, |
| 582 | +public datasets that are registered in Gaia Catalog can be “staged”: |
| 583 | +transformed and then loaded as tables in a standardized |
| 584 | +Entity-Attribute-Value format. Other geospatial data, such as geocoded |
| 585 | +addresses, can also be loaded into the staging database for use in |
| 586 | +conjunction with the staged data.</p> |
| 587 | +<p>All operations on the staging database (creating tables, inserting |
| 588 | +data, accessing data, etc.) are performed through the “execution |
| 589 | +engine”. The execution engine can be any software package (e.g. R |
| 590 | +package, Python library, CLI) that connects to the database and |
| 591 | +functionalizes the logic required to write or read data to and from the |
| 592 | +standard format. Currently, there is one execution engine: an R Package |
| 593 | +named <a href="gaiaCore/index.html">gaiaCore</a>.</p> |
| 594 | +<hr /> |
| 595 | +<p><br></p> |
| 596 | +</div> |
| 597 | +<div id="extensions" class="section level2"> |
| 598 | +<h2><a href="gaia-extensions.html">Extensions</a></h2> |
| 599 | +<p>Any functionality that falls outside of Gaia Core’s scope (basic |
| 600 | +Create, Read, Update and Delete operations) can be encapsulated in an |
| 601 | +Extension. An extension can be thought of as a software package or |
| 602 | +library that interfaces with Gaia Core (through the execution engine) |
| 603 | +that collects similar functionality. Extensions can be grouped by the |
| 604 | +communities they serve or by the functionality they provide. For |
| 605 | +example, the <a href="gaia-extensions-ohdsi.html">gaiaOHDSI |
| 606 | +extension</a> is built to provide members of the OHDSI community useful |
| 607 | +connectors between Gaia Core and an OMOP database and various OHDSI |
| 608 | +tools. On the other hand, general (hypothetical) extensions like gaiaVis |
| 609 | +or gaiaLayer provide visualization and layer building software to Gaia |
| 610 | +Core, respectively.</p> |
| 611 | +</div> |
| 612 | +</div> |
604 | 613 |
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