add sources field to MetaEdge so that infores identifiers are returne… - #430

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add sources field to MetaEdge so that infores identifiers are returne…#430
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This PR adds the sources field to MetaEdge so that infores identifiers are returned in the meta knowledge graph.

Recently, the modeling and TAQA teams were presented with the use case:
"Find me all the unique triples provided to Translator by SEMMEDDB"

We know that SEMMEDDB is currently being served by both BTE and RTX-KG2. Some questions we wanted to ask with code:

  • Are there any other SEMMEDDB edges in Translator not from these two aggregators?
  • What are the unique SPOQs that we can expect BTE to provide from SEMMEDDB, how about RTX-KG2?
  • Do SPOQs from RTX-KG2 (and ultimately SEMMEDDB) match those provided from BTE (via SEMMEDDB)?

Note: we also have several instances of Chembl and clinicaltrials.gov being ingested by multiple teams. It would be handy for the modeling team to be able to compare translations of these important sources between groups (with the ultimate goal of having one transform schema per ingest that groups could follow to keep ingests consistent).

If testing software finds edges in the metakg that need to change with Biolink releases, it would be very handy for QC to be able to point to the primary_knowledge_source (or sources) for more information.

If not for 1.4, then perhaps this could be considered for the next release.

@sierra-moxon
added a 'MUST' statement for providing primary_knowledge_source in at…
9ffdaf3
… least one RetrievalSource member of the sources list on both Edges and MetaEdges
edeutsch
edeutsch reviewed Apr 27, 2023
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I think this is a reasonable addition, but I question if we can tolerate to make a mandatory (and thus breaking) addition at this late stage of 1.4. I would be happier with making it optional in 1.4 and mandatory in 1.5 is we so desire.

@edeutschedeutsch added this to the v1.4 milestone Apr 27, 2023
@edeutschedeutsch modified the milestones: v1.4, v1.5May 23, 2023
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@RichardBruskiewichRichardBruskiewichRichardBruskiewich approved these changes
@edeutschedeutschedeutsch approved these changes
@vdancikvdancikvdancik approved these changes
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
add sources field to MetaEdge so that infores identifiers are returne… - #430
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sierra-moxon wants to merge 3 commits into
1.4from 
add_sources_to_meta_edge
Open
add sources field to MetaEdge so that infores identifiers are returne…#430
sierra-moxon wants to merge 3 commits into
1.4from 
add_sources_to_meta_edge
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This PR adds the sources field to MetaEdge so that infores identifiers are returned in the meta knowledge graph.
Recently, the modeling and TAQA teams were presented with the use case:

"Find me all the unique triples provided to Translator by SEMMEDDB"
We know that SEMMEDDB is currently being served by both BTE and RTX-KG2. Some questions we wanted to ask with code:
  • Are there any other SEMMEDDB edges in Translator not from these two aggregators?
  • What are the unique SPOQs that we can expect BTE to provide from SEMMEDDB, how about RTX-KG2?
  • Do SPOQs from RTX-KG2 (and ultimately SEMMEDDB) match those provided from BTE (via SEMMEDDB)?
Note: we also have several instances of Chembl and clinicaltrials.gov being ingested by multiple teams. It would be handy for the modeling team to be able to compare translations of these important sources between groups (with the ultimate goal of having one transform schema per ingest that groups could follow to keep ingests consistent).
If testing software finds edges in the metakg that need to change with Biolink releases, it would be very handy for QC to be able to point to the primary_knowledge_source (or sources) for more information.
If not for 1.4, then perhaps this could be considered for the next release.
@sierra-moxon
added a 'MUST' statement for providing primary_knowledge_source in at…
9ffdaf3
… least one RetrievalSource member of the sources list on both Edges and MetaEdges
edeutsch
edeutsch
reviewed
Apr 27, 2023
View reviewed changes
@edeutschedeutsch
left a comment
•

edited

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I think this is a reasonable addition, but I question if we can tolerate to make a mandatory (and thus breaking) addition at this late stage of 1.4. I would be happier with making it optional in 1.4 and mandatory in 1.5 is we so desire.
@edeutschedeutsch
added this to the v1.4 milestone
Apr 27, 2023
@edeutschedeutsch
modified the milestones:
v1.4, v1.5May 23, 2023
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Reviewers

@RichardBruskiewichRichardBruskiewichRichardBruskiewich approved these changes
@edeutschedeutschedeutsch approved these changes
@vdancikvdancikvdancik approved these changes
@mbrushmbrushAwaiting requested review from mbrush
@kennethmortonkennethmortonAwaiting requested review from kennethmorton
@andrewsuandrewsuAwaiting requested review from andrewsu
@brettasmibrettasmiAwaiting requested review from brettasmi
@MarkDWilliamsMarkDWilliamsAwaiting requested review from MarkDWilliams
@marcdubybroadmarcdubybroadAwaiting requested review from marcdubybroad
@webyrdwebyrdAwaiting requested review from webyrd
@vemonetvemonetAwaiting requested review from vemonet
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
add sources field to MetaEdge so that infores identifiers are returne… - #430
Open
sierra-moxon wants to merge 3 commits into
1.4from 
add_sources_to_meta_edge
Open
add sources field to MetaEdge so that infores identifiers are returne…#430
sierra-moxon wants to merge 3 commits into
1.4from 
add_sources_to_meta_edge
Conversation
@sierra-moxon
@sierra-moxonsierra-moxon
commented
Apr 24, 2023•

edited

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This PR adds the sources field to MetaEdge so that infores identifiers are returned in the meta knowledge graph.
Recently, the modeling and TAQA teams were presented with the use case:

"Find me all the unique triples provided to Translator by SEMMEDDB"
We know that SEMMEDDB is currently being served by both BTE and RTX-KG2. Some questions we wanted to ask with code:
  • Are there any other SEMMEDDB edges in Translator not from these two aggregators?
  • What are the unique SPOQs that we can expect BTE to provide from SEMMEDDB, how about RTX-KG2?
  • Do SPOQs from RTX-KG2 (and ultimately SEMMEDDB) match those provided from BTE (via SEMMEDDB)?
Note: we also have several instances of Chembl and clinicaltrials.gov being ingested by multiple teams. It would be handy for the modeling team to be able to compare translations of these important sources between groups (with the ultimate goal of having one transform schema per ingest that groups could follow to keep ingests consistent).
If testing software finds edges in the metakg that need to change with Biolink releases, it would be very handy for QC to be able to point to the primary_knowledge_source (or sources) for more information.
If not for 1.4, then perhaps this could be considered for the next release.
@sierra-moxon
added a 'MUST' statement for providing primary_knowledge_source in at…
9ffdaf3
… least one RetrievalSource member of the sources list on both Edges and MetaEdges
edeutsch
edeutsch
reviewed
Apr 27, 2023
View reviewed changes
@edeutschedeutsch
left a comment
•

edited

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I think this is a reasonable addition, but I question if we can tolerate to make a mandatory (and thus breaking) addition at this late stage of 1.4. I would be happier with making it optional in 1.4 and mandatory in 1.5 is we so desire.
@edeutschedeutsch
added this to the v1.4 milestone
Apr 27, 2023
@edeutschedeutsch
modified the milestones:
v1.4, v1.5May 23, 2023
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Reviewers

@RichardBruskiewichRichardBruskiewichRichardBruskiewich approved these changes
@edeutschedeutschedeutsch approved these changes
@vdancikvdancikvdancik approved these changes
@mbrushmbrushAwaiting requested review from mbrush
@kennethmortonkennethmortonAwaiting requested review from kennethmorton
@andrewsuandrewsuAwaiting requested review from andrewsu
@brettasmibrettasmiAwaiting requested review from brettasmi
@MarkDWilliamsMarkDWilliamsAwaiting requested review from MarkDWilliams
@marcdubybroadmarcdubybroadAwaiting requested review from marcdubybroad
@webyrdwebyrdAwaiting requested review from webyrd
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@gprice1129gprice1129Awaiting requested review from gprice1129
@yakaboskicyakaboskicAwaiting requested review from yakaboskic
@tziomicstziomicsAwaiting requested review from tziomics

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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
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} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
add sources field to MetaEdge so that infores identifiers are returne… - #430
Open
sierra-moxon wants to merge 3 commits into
1.4from 
add_sources_to_meta_edge
Open
add sources field to MetaEdge so that infores identifiers are returne…#430
sierra-moxon wants to merge 3 commits into
1.4from 
add_sources_to_meta_edge
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@sierra-moxonsierra-moxon
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Apr 24, 2023•

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This PR adds the sources field to MetaEdge so that infores identifiers are returned in the meta knowledge graph.
Recently, the modeling and TAQA teams were presented with the use case:

"Find me all the unique triples provided to Translator by SEMMEDDB"
We know that SEMMEDDB is currently being served by both BTE and RTX-KG2. Some questions we wanted to ask with code:
  • Are there any other SEMMEDDB edges in Translator not from these two aggregators?
  • What are the unique SPOQs that we can expect BTE to provide from SEMMEDDB, how about RTX-KG2?
  • Do SPOQs from RTX-KG2 (and ultimately SEMMEDDB) match those provided from BTE (via SEMMEDDB)?
Note: we also have several instances of Chembl and clinicaltrials.gov being ingested by multiple teams. It would be handy for the modeling team to be able to compare translations of these important sources between groups (with the ultimate goal of having one transform schema per ingest that groups could follow to keep ingests consistent).
If testing software finds edges in the metakg that need to change with Biolink releases, it would be very handy for QC to be able to point to the primary_knowledge_source (or sources) for more information.
If not for 1.4, then perhaps this could be considered for the next release.
@sierra-moxon
added a 'MUST' statement for providing primary_knowledge_source in at…
9ffdaf3
… least one RetrievalSource member of the sources list on both Edges and MetaEdges
edeutsch
edeutsch
reviewed
Apr 27, 2023
View reviewed changes
@edeutschedeutsch
left a comment
•

edited

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I think this is a reasonable addition, but I question if we can tolerate to make a mandatory (and thus breaking) addition at this late stage of 1.4. I would be happier with making it optional in 1.4 and mandatory in 1.5 is we so desire.
@edeutschedeutsch
added this to the v1.4 milestone
Apr 27, 2023
@edeutschedeutsch
modified the milestones:
v1.4, v1.5May 23, 2023
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@RichardBruskiewichRichardBruskiewichRichardBruskiewich approved these changes
@edeutschedeutschedeutsch approved these changes
@vdancikvdancikvdancik approved these changes
@mbrushmbrushAwaiting requested review from mbrush
@kennethmortonkennethmortonAwaiting requested review from kennethmorton
@andrewsuandrewsuAwaiting requested review from andrewsu
@brettasmibrettasmiAwaiting requested review from brettasmi
@MarkDWilliamsMarkDWilliamsAwaiting requested review from MarkDWilliams
@marcdubybroadmarcdubybroadAwaiting requested review from marcdubybroad
@webyrdwebyrdAwaiting requested review from webyrd
@vemonetvemonetAwaiting requested review from vemonet
@gprice1129gprice1129Awaiting requested review from gprice1129
@yakaboskicyakaboskicAwaiting requested review from yakaboskic
@tziomicstziomicsAwaiting requested review from tziomics

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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
add sources field to MetaEdge so that infores identifiers are returne… - #430
Open
sierra-moxon wants to merge 3 commits into
1.4from 
add_sources_to_meta_edge
Open
add sources field to MetaEdge so that infores identifiers are returne…#430
sierra-moxon wants to merge 3 commits into
1.4from 
add_sources_to_meta_edge
Conversation
@sierra-moxon
@sierra-moxonsierra-moxon
commented
Apr 24, 2023•

edited

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This PR adds the sources field to MetaEdge so that infores identifiers are returned in the meta knowledge graph.
Recently, the modeling and TAQA teams were presented with the use case:

"Find me all the unique triples provided to Translator by SEMMEDDB"
We know that SEMMEDDB is currently being served by both BTE and RTX-KG2. Some questions we wanted to ask with code:
  • Are there any other SEMMEDDB edges in Translator not from these two aggregators?
  • What are the unique SPOQs that we can expect BTE to provide from SEMMEDDB, how about RTX-KG2?
  • Do SPOQs from RTX-KG2 (and ultimately SEMMEDDB) match those provided from BTE (via SEMMEDDB)?
Note: we also have several instances of Chembl and clinicaltrials.gov being ingested by multiple teams. It would be handy for the modeling team to be able to compare translations of these important sources between groups (with the ultimate goal of having one transform schema per ingest that groups could follow to keep ingests consistent).
If testing software finds edges in the metakg that need to change with Biolink releases, it would be very handy for QC to be able to point to the primary_knowledge_source (or sources) for more information.
If not for 1.4, then perhaps this could be considered for the next release.
@sierra-moxon
added a 'MUST' statement for providing primary_knowledge_source in at…
9ffdaf3
… least one RetrievalSource member of the sources list on both Edges and MetaEdges
edeutsch
edeutsch
reviewed
Apr 27, 2023
View reviewed changes
@edeutschedeutsch
left a comment
•

edited

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I think this is a reasonable addition, but I question if we can tolerate to make a mandatory (and thus breaking) addition at this late stage of 1.4. I would be happier with making it optional in 1.4 and mandatory in 1.5 is we so desire.
@edeutschedeutsch
added this to the v1.4 milestone
Apr 27, 2023
@edeutschedeutsch
modified the milestones:
v1.4, v1.5May 23, 2023
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Reviewers

@RichardBruskiewichRichardBruskiewichRichardBruskiewich approved these changes
@edeutschedeutschedeutsch approved these changes
@vdancikvdancikvdancik approved these changes
@mbrushmbrushAwaiting requested review from mbrush
@kennethmortonkennethmortonAwaiting requested review from kennethmorton
@andrewsuandrewsuAwaiting requested review from andrewsu
@brettasmibrettasmiAwaiting requested review from brettasmi
@MarkDWilliamsMarkDWilliamsAwaiting requested review from MarkDWilliams
@marcdubybroadmarcdubybroadAwaiting requested review from marcdubybroad
@webyrdwebyrdAwaiting requested review from webyrd
@vemonetvemonetAwaiting requested review from vemonet
@gprice1129gprice1129Awaiting requested review from gprice1129
@yakaboskicyakaboskicAwaiting requested review from yakaboskic
@tziomicstziomicsAwaiting requested review from tziomics

+1 more reviewer

@edgargaticaCUedgargaticaCUedgargaticaCU approved these changes
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
add sources field to MetaEdge so that infores identifiers are returne… - #430
Open
sierra-moxon wants to merge 3 commits into
1.4from 
add_sources_to_meta_edge
Open
add sources field to MetaEdge so that infores identifiers are returne…#430
sierra-moxon wants to merge 3 commits into
1.4from 
add_sources_to_meta_edge
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@sierra-moxon
@sierra-moxonsierra-moxon
commented
Apr 24, 2023•

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This PR adds the sources field to MetaEdge so that infores identifiers are returned in the meta knowledge graph.
Recently, the modeling and TAQA teams were presented with the use case:

"Find me all the unique triples provided to Translator by SEMMEDDB"
We know that SEMMEDDB is currently being served by both BTE and RTX-KG2. Some questions we wanted to ask with code:
  • Are there any other SEMMEDDB edges in Translator not from these two aggregators?
  • What are the unique SPOQs that we can expect BTE to provide from SEMMEDDB, how about RTX-KG2?
  • Do SPOQs from RTX-KG2 (and ultimately SEMMEDDB) match those provided from BTE (via SEMMEDDB)?
Note: we also have several instances of Chembl and clinicaltrials.gov being ingested by multiple teams. It would be handy for the modeling team to be able to compare translations of these important sources between groups (with the ultimate goal of having one transform schema per ingest that groups could follow to keep ingests consistent).
If testing software finds edges in the metakg that need to change with Biolink releases, it would be very handy for QC to be able to point to the primary_knowledge_source (or sources) for more information.
If not for 1.4, then perhaps this could be considered for the next release.
@sierra-moxon
added a 'MUST' statement for providing primary_knowledge_source in at…
9ffdaf3
… least one RetrievalSource member of the sources list on both Edges and MetaEdges
edeutsch
edeutsch
reviewed
Apr 27, 2023
View reviewed changes
@edeutschedeutsch
left a comment
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I think this is a reasonable addition, but I question if we can tolerate to make a mandatory (and thus breaking) addition at this late stage of 1.4. I would be happier with making it optional in 1.4 and mandatory in 1.5 is we so desire.
@edeutschedeutsch
added this to the v1.4 milestone
Apr 27, 2023
@edeutschedeutsch
modified the milestones:
v1.4, v1.5May 23, 2023
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@RichardBruskiewichRichardBruskiewichRichardBruskiewich approved these changes
@edeutschedeutschedeutsch approved these changes
@vdancikvdancikvdancik approved these changes
@mbrushmbrushAwaiting requested review from mbrush
@kennethmortonkennethmortonAwaiting requested review from kennethmorton
@andrewsuandrewsuAwaiting requested review from andrewsu
@brettasmibrettasmiAwaiting requested review from brettasmi
@MarkDWilliamsMarkDWilliamsAwaiting requested review from MarkDWilliams
@marcdubybroadmarcdubybroadAwaiting requested review from marcdubybroad
@webyrdwebyrdAwaiting requested review from webyrd
@vemonetvemonetAwaiting requested review from vemonet
@gprice1129gprice1129Awaiting requested review from gprice1129
@yakaboskicyakaboskicAwaiting requested review from yakaboskic
@tziomicstziomicsAwaiting requested review from tziomics

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@edgargaticaCUedgargaticaCUedgargaticaCU approved these changes
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@sierra-moxon@RichardBruskiewich@edeutsch@vdancik@edgargaticaCU

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
add sources field to MetaEdge so that infores identifiers are returne… - #430
Open
sierra-moxon wants to merge 3 commits into
1.4from 
add_sources_to_meta_edge
Open
add sources field to MetaEdge so that infores identifiers are returne…#430
sierra-moxon wants to merge 3 commits into
1.4from 
add_sources_to_meta_edge
Conversation
@sierra-moxon
@sierra-moxonsierra-moxon
commented
Apr 24, 2023•

edited

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This PR adds the sources field to MetaEdge so that infores identifiers are returned in the meta knowledge graph.
Recently, the modeling and TAQA teams were presented with the use case:

"Find me all the unique triples provided to Translator by SEMMEDDB"
We know that SEMMEDDB is currently being served by both BTE and RTX-KG2. Some questions we wanted to ask with code:
  • Are there any other SEMMEDDB edges in Translator not from these two aggregators?
  • What are the unique SPOQs that we can expect BTE to provide from SEMMEDDB, how about RTX-KG2?
  • Do SPOQs from RTX-KG2 (and ultimately SEMMEDDB) match those provided from BTE (via SEMMEDDB)?
Note: we also have several instances of Chembl and clinicaltrials.gov being ingested by multiple teams. It would be handy for the modeling team to be able to compare translations of these important sources between groups (with the ultimate goal of having one transform schema per ingest that groups could follow to keep ingests consistent).
If testing software finds edges in the metakg that need to change with Biolink releases, it would be very handy for QC to be able to point to the primary_knowledge_source (or sources) for more information.
If not for 1.4, then perhaps this could be considered for the next release.
@sierra-moxon
added a 'MUST' statement for providing primary_knowledge_source in at…
9ffdaf3
… least one RetrievalSource member of the sources list on both Edges and MetaEdges
edeutsch
edeutsch
reviewed
Apr 27, 2023
View reviewed changes
@edeutschedeutsch
left a comment
•

edited

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I think this is a reasonable addition, but I question if we can tolerate to make a mandatory (and thus breaking) addition at this late stage of 1.4. I would be happier with making it optional in 1.4 and mandatory in 1.5 is we so desire.
@edeutschedeutsch
added this to the v1.4 milestone
Apr 27, 2023
@edeutschedeutsch
modified the milestones:
v1.4, v1.5May 23, 2023
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Reviewers

@RichardBruskiewichRichardBruskiewichRichardBruskiewich approved these changes
@edeutschedeutschedeutsch approved these changes
@vdancikvdancikvdancik approved these changes
@mbrushmbrushAwaiting requested review from mbrush
@kennethmortonkennethmortonAwaiting requested review from kennethmorton
@andrewsuandrewsuAwaiting requested review from andrewsu
@brettasmibrettasmiAwaiting requested review from brettasmi
@MarkDWilliamsMarkDWilliamsAwaiting requested review from MarkDWilliams
@marcdubybroadmarcdubybroadAwaiting requested review from marcdubybroad
@webyrdwebyrdAwaiting requested review from webyrd
@vemonetvemonetAwaiting requested review from vemonet
@gprice1129gprice1129Awaiting requested review from gprice1129
@yakaboskicyakaboskicAwaiting requested review from yakaboskic
@tziomicstziomicsAwaiting requested review from tziomics

+1 more reviewer

@edgargaticaCUedgargaticaCUedgargaticaCU approved these changes
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5 participants

@sierra-moxon@RichardBruskiewich@edeutsch@vdancik@edgargaticaCU

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
add sources field to MetaEdge so that infores identifiers are returne… - #430
Open
sierra-moxon wants to merge 3 commits into
1.4from 
add_sources_to_meta_edge
Open
add sources field to MetaEdge so that infores identifiers are returne…#430
sierra-moxon wants to merge 3 commits into
1.4from 
add_sources_to_meta_edge
Conversation
@sierra-moxon
@sierra-moxonsierra-moxon
commented
Apr 24, 2023•

edited

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Member
This PR adds the sources field to MetaEdge so that infores identifiers are returned in the meta knowledge graph.
Recently, the modeling and TAQA teams were presented with the use case:

"Find me all the unique triples provided to Translator by SEMMEDDB"
We know that SEMMEDDB is currently being served by both BTE and RTX-KG2. Some questions we wanted to ask with code:
  • Are there any other SEMMEDDB edges in Translator not from these two aggregators?
  • What are the unique SPOQs that we can expect BTE to provide from SEMMEDDB, how about RTX-KG2?
  • Do SPOQs from RTX-KG2 (and ultimately SEMMEDDB) match those provided from BTE (via SEMMEDDB)?
Note: we also have several instances of Chembl and clinicaltrials.gov being ingested by multiple teams. It would be handy for the modeling team to be able to compare translations of these important sources between groups (with the ultimate goal of having one transform schema per ingest that groups could follow to keep ingests consistent).
If testing software finds edges in the metakg that need to change with Biolink releases, it would be very handy for QC to be able to point to the primary_knowledge_source (or sources) for more information.
If not for 1.4, then perhaps this could be considered for the next release.
@sierra-moxon
added a 'MUST' statement for providing primary_knowledge_source in at…
9ffdaf3
… least one RetrievalSource member of the sources list on both Edges and MetaEdges
edeutsch
edeutsch
reviewed
Apr 27, 2023
View reviewed changes
@edeutschedeutsch
left a comment
•

edited

Loading

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I think this is a reasonable addition, but I question if we can tolerate to make a mandatory (and thus breaking) addition at this late stage of 1.4. I would be happier with making it optional in 1.4 and mandatory in 1.5 is we so desire.
@edeutschedeutsch
added this to the v1.4 milestone
Apr 27, 2023
@edeutschedeutsch
modified the milestones:
v1.4, v1.5May 23, 2023
Sign up for freeto join this conversation on GitHub.
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Reviewers

@RichardBruskiewichRichardBruskiewichRichardBruskiewich approved these changes
@edeutschedeutschedeutsch approved these changes
@vdancikvdancikvdancik approved these changes
@mbrushmbrushAwaiting requested review from mbrush
@kennethmortonkennethmortonAwaiting requested review from kennethmorton
@andrewsuandrewsuAwaiting requested review from andrewsu
@brettasmibrettasmiAwaiting requested review from brettasmi
@MarkDWilliamsMarkDWilliamsAwaiting requested review from MarkDWilliams
@marcdubybroadmarcdubybroadAwaiting requested review from marcdubybroad
@webyrdwebyrdAwaiting requested review from webyrd
@vemonetvemonetAwaiting requested review from vemonet
@gprice1129gprice1129Awaiting requested review from gprice1129
@yakaboskicyakaboskicAwaiting requested review from yakaboskic
@tziomicstziomicsAwaiting requested review from tziomics

+1 more reviewer

@edgargaticaCUedgargaticaCUedgargaticaCU approved these changes
Reviewers whose approvals may not affect merge requirements

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Milestone

v1.5

Development

Successfully merging this pull request may close these issues.

5 participants

@sierra-moxon@RichardBruskiewich@edeutsch@vdancik@edgargaticaCU