Refactoring for GitHub Docs hosting.

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-"<br><font size='6px'>Guesdt</font><br><br>Visualize, search, and understand hundreds of millions of concepts, codes, terms, definitions, semantic types and relationships. Guesdt now uses the <a href='https://ubkg.docs.xconsortia.org'>Unified Biomedical Knowledge Graph</a> (UBKG) API as its backend data source including the U.S. National Library of Medicine's <a href='https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/index.html'>Unified Medical Language System</a> (UMLS) Metathesaurus in an updated, more efficient schema, thanks to support from National Institute's of Health Common Fund consortia. Follow the links above for the respective licenses and attributions. <br><br><form onsubmit='LaunchGuesdt(Server.value.toString(),UMLSKey.value.toString());'><label for='Server'>Server:</label> <input type='text' id='Server' name='Server' value='https://ontology.api.hubmapconsortium.org' size='40'> <label for='UMLSKey'> UMLS-Key: </label> <input type='text' id='UMLSKey' name='UMLSKey' size='40'> <input type='submit' value='Submit'></form><br>Launch the Guesdt application in your browser by authenticating above with your <a href='https://uts.nlm.nih.gov'>NLM UTS</a> profile API key and explore relationships among medical, genomic, pharmaceutical, or any other concepts across <a href='https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html'>more than 200 source vocabularies</a> of UMLS and <a href='https://ubkg.docs.xconsortia.org/contexts/'>many more from UBKG</a>. If you don't have a UTS account, getting one is free, quick, and now there's a reason to do it.<br><br>The embedded PDF reader below shows a vector graphic of Guesdt in Safari captured via 'Print...PDF'. The <a href='#userguide'>Guesdt user guide</a> explains this and all other features.<br><embed src='NivDemo.pdf' width='"+(w-50)+"px' height='"+((w-50)/2)+"px' /> <br>UMLS's schema elegantly simplification in Guesdt will instantly broaden and refine your understanding. There is always more to discover, particularly where concepts interweave among vocabularies. The combination is far greater than the sum of its parts, but UMLS has been too complex for individuals to conceive. Now modern technology makes possible interactive graphing of UMLS, with many more features to come. Guesdt is meant to reveal future pathways, not to be an exclusive destination. Use it and remix it.<br><br>After many decades work by some of the greatest leaders in our field, UMLS is now computable at scale. Guesdt is the result of dedication to the idea that individuals need to understand this complex web of concepts in order to most effectively use it and realize its vast potential. Guesdt, with a silent d, stands for Graphing UMLS Enables Search in Dynamic Trees. <br><br><a id='userguide'><font size='5px'>User Guide</font></a><br>This guide is intended to be used only as reference. Just use the application by typing, clicking, dragging, scrolling; it will reveal its features. If you must, keep reading.<br><br><font size='4px'>Definitions:</font><br><strong>Concept:</strong> UMLS (or imputed) unique identifier (CUI) and its preferred string. Each concept may have many codes. Concepts also have exactly one preferred term, optional definitions, and semantic types.<br><strong>Code:</strong> source vocabulary unique identifier for a concept (presented as source vocabulary abbreviation, a colon, and its source code). Each code may have many terms.<br><strong>Term:</strong> string for a code. Thus, concepts have codes which have terms.<br><strong>Relations:</strong> There are two types of relations, both drawn as light gray lines. <strong>Relations asserted between vocabularies:</strong> shown in upper case when codes from two source vocabularies share the same concept. The relation name is shown as the source vocabulary abbreviation defined by UMLS and UBKG, such as RXNORM. <strong>Relations asserted within one vocabulary:</strong> shown in lower case are read from right to left (the child node, the relation, and then the parent node).<br><strong>Node:</strong> A node in the graph is a relation, a circle, and its concept preferred term.<br><strong>Default code:</strong> The default code FMA:7149. The application opens with this code stating its terms and visualizing its relations.<br><strong>Semantic types:</strong> UMLS concepts includes semantic types of the concept (seen via clicking on a circle).<br><br><font size='4px'>Available textual interactions:</font><br><strong>Search:</strong> Type in an idea you wish to explore in the term input and click the Term->Codes button. This compares the input to all terms in Guesdt and will return a set of codes, term types, and terms.<br><strong>Clicking on any code or term in the results:</strong> will load it into its corresponding input.<br><strong>Restart the viz from the selected code:</strong> does what it says, typically used after a term search and code selection.<br><strong>Show terms of a code:</strong> Enter a code (vocabulary abbreviation colon code) or obtain it from right-click on a node and click the Code->Terms button.<br><strong>General considerations:</strong> These textual interactions can be used in various combinations to explore using text alone. Note also that the results are displayed for easy copying into a spreadsheet for further analysis. Some searches, particularly richly connected codes from large vocabularies may slow results return. If a result does not return, just continue doing something else.<br><br><font size='4px'>Available visual interactions:</font><br><strong>Click on a relation:</strong> Cross-vocabulary relations (upper case) will open a browser tab with load the source information into the text window or if from UMLS then the description of that vocabulary from NLM in another tab. Clicking an in vocabulary relation (lower case) will collapse all other identical relations extending visually from that node to one relation to reduce visual clutter. It will turn that selected single relation red in color. Clicking again will show all the others again and revert the color. Multiple relation types can each be collapsed in this way to streamline a desired visualization.<br><strong>Click on a circle:</strong> will show the complete information regarding that concept across all vocabularies with the concept ID, codes, terms, definitions, and semantic types.<br><strong>Click on a node name:</strong> this is the principal interaction which opens the related nodes of a node. Related nodes are of each of the two relation types discussed above, in vocabulary and concepts shared in other vocabularies. Some nodes may have a delay before opening if they have to request MANY relationships from the backend. Clicking again will close the related nodes of a node.<br><strong>Scrolling:</strong> will zoom the visualization smaller and larger centered on the mouse location. Note also double-click and shift double-click also zoom.<br><strong>Drag:</strong> to pan the visualization.<br><strong>Browser functions:</strong> such as copy-paste from inputs, find, back, reload, and print are optimized. The best way to save a visualization is to zoom it down to fit on a page and print it to a PDF. As a vector graphic, it can be re-zoomed without visual loss.<br><strong>Dismiss:</strong> this button hides the text interaction page. It can be re-shown by click on any node circle (which will also load the content of that concept).<br><br><font size='4px'>Other visual feedback:</font><br><strong>Red circles:</strong> this concept in this vocabulary has been seen elsewhere in the current visualization (both the original and replica turns red). Use caution opening it. Consider opening the other one further toward the root to avoid too many blue lines.<br><strong>Blue lines:</strong> are drawn between instances of the same concept in the same vocabulary (the red replica circles). These links are often the most revealing discoveries. Because of the multiple hierarchies and the fact that relations include both parents and children, to avoid clutter, blue lines are not drawn among replicas that are grandchildren or uncles or aunts. Those replica circles are still turned red. <br><strong>MANY:</strong> Whenever there are more than 64 relations from the same code known to the visualization, it is shown with the text in red.<br><br><font size='-1px'>This site owner is authorized to distribute UMLS to licensees. This authority is provable because the application will launch only after a valid authentication via UTS. Per NLM recommended approach, this site uses its own API to securely combine UTS credentials with its distributor license to verify against NLM API. UTS credentials are not seen by Guesdt.com. If after using this site you have any concerns, you can change your UTS password. The Creative Commons License below refers to the software only, not to the vocabulary content or to its distribution which is governed by NLM and the other sources.<br><br><a rel='license' href='http://creativecommons.org/licenses/by/4.0/'><img alt='Creative Commons License' style='border-width:0' src='https://i.creativecommons.org/l/by/4.0/80x15.png' /></a><span xmlns:dct='http://purl.org/dc/terms/' property='dct:title'> Guesdt</span> by <a xmlns:cc='http://creativecommons.org/ns#' href='http://www.computationdoc.com' property='cc:attributionName' rel='cc:attributionURL'>Jonathan C. Silverstein</a> is licensed under a <a rel='license' href='http://creativecommons.org/licenses/by/4.0/''>Creative Commons Attribution 4.0 International License</a>. Based on a work at <a xmlns:dct='http://purl.org/dc/terms/' href='https://d3js.org' rel='dct:source'>https://d3js.org</a>.</font>"
+"<br><font size='6px'>Guesdt</font><br><br>Visualize, search, and understand hundreds of millions of concepts, codes, terms, definitions, semantic types and relationships. Guesdt now uses the <a href='https://ubkg.docs.xconsortia.org'>Unified Biomedical Knowledge Graph</a> (UBKG) API as its backend data source including the U.S. National Library of Medicine's <a href='https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/index.html'>Unified Medical Language System</a> (UMLS) Metathesaurus in an updated, more efficient schema, thanks to support from National Institute's of Health Common Fund consortia. Follow the links above for the respective licenses and attributions. <br><br><form onsubmit='LaunchGuesdt(Server.value.toString(),UMLSKey.value.toString());'><label for='Server'>Server:</label> <input type='text' id='Server' name='Server' value='https://datadistillery.api.sennetconsortium.org/' size='40'> <label for='UMLSKey'> UMLS-Key: </label> <input type='text' id='UMLSKey' name='UMLSKey' size='40'> <input type='submit' value='Submit'></form><br>Launch the Guesdt application in your browser by authenticating above with your <a href='https://uts.nlm.nih.gov'>NLM UTS</a> profile API key and explore relationships among medical, genomic, pharmaceutical, or any other concepts across <a href='https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html'>more than 200 source vocabularies</a> of UMLS and <a href='https://ubkg.docs.xconsortia.org/contexts/'>many more from UBKG</a>. If you don't have a UTS account, getting one is free, quick, and now there's a reason to do it.<br><br>The embedded PDF reader below shows a vector graphic of Guesdt in Safari captured via 'Print...PDF'. The <a href='#userguide'>Guesdt user guide</a> explains this and all other features.<br><embed src='NivDemo.pdf' width='"+(w-50)+"px' height='"+((w-50)/2)+"px' /> <br>UMLS's schema elegantly simplification in Guesdt will instantly broaden and refine your understanding. There is always more to discover, particularly where concepts interweave among vocabularies. The combination is far greater than the sum of its parts, but UMLS has been too complex for individuals to conceive. Now modern technology makes possible interactive graphing of UMLS, with many more features to come. Guesdt is meant to reveal future pathways, not to be an exclusive destination. Use it and remix it.<br><br>After many decades work by some of the greatest leaders in our field, UMLS is now computable at scale. Guesdt is the result of dedication to the idea that individuals need to understand this complex web of concepts in order to most effectively use it and realize its vast potential. Guesdt, with a silent d, stands for Graphing UMLS Enables Search in Dynamic Trees. <br><br><a id='userguide'><font size='5px'>User Guide</font></a><br>This guide is intended to be used only as reference. Just use the application by typing, clicking, dragging, scrolling; it will reveal its features. If you must, keep reading.<br><br><font size='4px'>Definitions:</font><br><strong>Concept:</strong> UMLS (or imputed) unique identifier (CUI) and its preferred string. Each concept may have many codes. Concepts also have exactly one preferred term, optional definitions, and semantic types.<br><strong>Code:</strong> source vocabulary unique identifier for a concept (presented as source vocabulary abbreviation, a colon, and its source code). Each code may have many terms.<br><strong>Term:</strong> string for a code. Thus, concepts have codes which have terms.<br><strong>Relations:</strong> There are two types of relations, both drawn as light gray lines. <strong>Relations asserted between vocabularies:</strong> shown in upper case when codes from two source vocabularies share the same concept. The relation name is shown as the source vocabulary abbreviation defined by UMLS and UBKG, such as RXNORM. <strong>Relations asserted within one vocabulary:</strong> shown in lower case are read from right to left (the child node, the relation, and then the parent node).<br><strong>Node:</strong> A node in the graph is a relation, a circle, and its concept preferred term.<br><strong>Default code:</strong> The default code FMA:7149. The application opens with this code stating its terms and visualizing its relations.<br><strong>Semantic types:</strong> UMLS concepts includes semantic types of the concept (seen via clicking on a circle).<br><br><font size='4px'>Available textual interactions:</font><br><strong>Search:</strong> Type in an idea you wish to explore in the term input and click the Term->Codes button. This compares the input to all terms in Guesdt and will return a set of codes, term types, and terms.<br><strong>Clicking on any code or term in the results:</strong> will load it into its corresponding input.<br><strong>Restart the viz from the selected code:</strong> does what it says, typically used after a term search and code selection.<br><strong>Show terms of a code:</strong> Enter a code (vocabulary abbreviation colon code) or obtain it from right-click on a node and click the Code->Terms button.<br><strong>General considerations:</strong> These textual interactions can be used in various combinations to explore using text alone. Note also that the results are displayed for easy copying into a spreadsheet for further analysis. Some searches, particularly richly connected codes from large vocabularies may slow results return. If a result does not return, just continue doing something else.<br><br><font size='4px'>Available visual interactions:</font><br><strong>Click on a relation:</strong> Cross-vocabulary relations (upper case) will open a browser tab with load the source information into the text window or if from UMLS then the description of that vocabulary from NLM in another tab. Clicking an in vocabulary relation (lower case) will collapse all other identical relations extending visually from that node to one relation to reduce visual clutter. It will turn that selected single relation red in color. Clicking again will show all the others again and revert the color. Multiple relation types can each be collapsed in this way to streamline a desired visualization.<br><strong>Click on a circle:</strong> will show the complete information regarding that concept across all vocabularies with the concept ID, codes, terms, definitions, and semantic types.<br><strong>Click on a node name:</strong> this is the principal interaction which opens the related nodes of a node. Related nodes are of each of the two relation types discussed above, in vocabulary and concepts shared in other vocabularies. Some nodes may have a delay before opening if they have to request MANY relationships from the backend. Clicking again will close the related nodes of a node.<br><strong>Scrolling:</strong> will zoom the visualization smaller and larger centered on the mouse location. Note also double-click and shift double-click also zoom.<br><strong>Drag:</strong> to pan the visualization.<br><strong>Browser functions:</strong> such as copy-paste from inputs, find, back, reload, and print are optimized. The best way to save a visualization is to zoom it down to fit on a page and print it to a PDF. As a vector graphic, it can be re-zoomed without visual loss.<br><strong>Dismiss:</strong> this button hides the text interaction page. It can be re-shown by click on any node circle (which will also load the content of that concept).<br><br><font size='4px'>Other visual feedback:</font><br><strong>Red circles:</strong> this concept in this vocabulary has been seen elsewhere in the current visualization (both the original and replica turns red). Use caution opening it. Consider opening the other one further toward the root to avoid too many blue lines.<br><strong>Blue lines:</strong> are drawn between instances of the same concept in the same vocabulary (the red replica circles). These links are often the most revealing discoveries. Because of the multiple hierarchies and the fact that relations include both parents and children, to avoid clutter, blue lines are not drawn among replicas that are grandchildren or uncles or aunts. Those replica circles are still turned red. <br><strong>MANY:</strong> Whenever there are more than 64 relations from the same code known to the visualization, it is shown with the text in red.<br><br><font size='-1px'>This site owner is authorized to distribute UMLS to licensees. This authority is provable because the application will launch only after a valid authentication via UTS. Per NLM recommended approach, this site uses its own API to securely combine UTS credentials with its distributor license to verify against NLM API. UTS credentials are not seen by Guesdt.com. If after using this site you have any concerns, you can change your UTS password. The Creative Commons License below refers to the software only, not to the vocabulary content or to its distribution which is governed by NLM and the other sources.<br><br><a rel='license' href='http://creativecommons.org/licenses/by/4.0/'><img alt='Creative Commons License' style='border-width:0' src='https://i.creativecommons.org/l/by/4.0/80x15.png' /></a><span xmlns:dct='http://purl.org/dc/terms/' property='dct:title'> Guesdt</span> by <a xmlns:cc='http://creativecommons.org/ns#' href='http://www.computationdoc.com' property='cc:attributionName' rel='cc:attributionURL'>Jonathan C. Silverstein</a> is licensed under a <a rel='license' href='http://creativecommons.org/licenses/by/4.0/''>Creative Commons Attribution 4.0 International License</a>. Based on a work at <a xmlns:dct='http://purl.org/dc/terms/' href='https://d3js.org' rel='dct:source'>https://d3js.org</a>.</font>"
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