1|GLYG-1340|API for ID mapping
1|GLYG-1410|API changes for cell line, tissue data
1|GLYG-1413|API changes for ID tracking data on glycan page
1|GLYG-1414|API changes for ID tracking data on protein page
1|GLYG-1427|Support disease synonymes in simple search
1|GLYG-1428|Support disease synonymes in global search
1|GLYG-1422|Simple and global search by glycan names
1|GLYG-1421|API changes to search by glycosylation type in protein simple search
1|GLYG-1420|API changes to search by glycosylation type in protein advanced search
1|GLYG-1332|API changes for proteoform data (PRO data) --> check after data push
1|GLYG-1419|API changes for proteoform crossref --> check after data push
1|GLYG-1417|Modular implementation of scoring scheme
1|GLYG-1418|Spec and API changes for Scoring
1|GLYG-X|idtracking property in glycan/protein detail response
1|GLYG-X|input_idlist should be string by comma
1|GLYG-X|organism will not be required
1|GLYG-X|idmapping search response: from, to, anchor --- top level legends
1|GLYG-X|unmapped change to object least ("inputid":"xx", "reason":"invalid xxx")

1|GLYG-XXX|include glycosylation types in protein search init
1|GLYG-XX|add "Gene" to "simple_search_category" property in /protein/search_init
1|GLYG-XXX|modify idmapping search method
1|GLYG-XX|create API for Nathan to get all published glytoucan list to production
?|GLYG-1407|Revise common search API (Supersearch)
1|GLYG-1408|Implement quick search init web service
1|GLYG-XX|sorting issue (sorting in one direction doesn't work)
1|GLYG-XX|avoid hit_score issues
1|GLYG-XX|Initial counts and list_ids for the supersearch


1|GLYG-1447|weekly|Process new data- glycan citations from ncfg
1|GLYG-1448|weekly|update glyconnect data (download link changed)
1|GLYG-1449|weekly|process new data - sandbox
1|GLYG-1458|weekly|update PubChem-ChEBI data (download link and processing process changed)
1|GLYG-1461|weekly|Generate CLO-Cellosaurus_id mapping file. (internal use)
1|GLYG-1462|weekly|Map cellosaurus_id to cell line name and clo_id
1|GLYG-1488|weekly|update unicarbkb download path


1|GLYG-1487|weekly|process disease data from glycosmos
1|GLYG-XXXX|input from file upload
1|GLYG-XXXX|talk to Dacian about docker startup
1|GLYG-XXXX|redeploy 1.7 frontend to beta prod
1|GLYG-XXXX|query in cacheinfo for idmapping
1|GLYG-XXXX|don't return list_id for motif in supersearch
1|GLYG-XXXX|result summary with supersearch list API
1|GLYG-XXXX|all list APIs should be the same (query obj) genelocus/orthologus

1|GLYG-1424|API changes to store glycosylation as range
0|GLYG-XXXX|contact email format issue

not-needed|GLYG-1425|API change to support glycosylation range in site view


1|GLYG-1494|Remove predicted glycosylation entries that have reported information
1|GLYG-1495|Adding the sequon for N-linked glycosites and sequon type
?|GLYG-1496|Changes in the SNV datasets
1|GLYG-1497|Update datasets
1|GLYG-1501|Change in xref_key xred_id for o_glcnac_mcw.csv 
1|GLYG-1498|Create sarscov2_protein_info_refseq.csv
1|GLYG-1499|Change in Tax ID
1|GLYG-1464|Change the default text in WebVOwl to reflect GlyGen details

1|GLYG-XXX|list_id for supsearch_init
1|GLYG-XXX|label from species to Organisms in superseaerch
1|GLYG-XXX|list of aggregation operators (NAND, NOR, AND, OR are basic required)
1|GLYG-XXX|order of conditions and concepts (sujeet will send example)



1|GLYG-XXX|P14210-1.294.294 site detail API missing all_sites (and others) properities  
1|GLYG-XXX|Make sure that glycosylation section has start_pos and end_pos in protein detail
1|GLYG-XXX|Descripancy between init paths and monogdb paths in supersearch
1|GLYG-XXX|Field name labels in supersearch init
1|GLYG-XXX|value for "id" show be lower case in supersearch init
1|GLYG-XXX|motif, site and enzyme concepts do not have fields
1|GLYG-XXX|species count in the supersearch init is 9 opposed to 7
1|GLYG-XXX|enzyme number is same as protein number in supersearch init (not correct)
1|GLYG-XXX|concept results merging startegy (AND vs OR)
1|GLYG-XXX|download protein list is failing



1|GLYG-XXX|idmapping list download (idmapping_mapped_list and idmapping_unmapped_list)
1|GLYG-XXX|when using species in query, use organism concept
?|GLYG-XXX|when using disease in query, use disease concept
1|GLYG-XXX|empty query supersearch should return entire/init numbers and list_ids
1|GLYG-XXX|return error code if unexpected query structure is submitted in supersearch


1|GLYG-XXX|motif_list download objects should be the same as motif_list response
1|GLYG-XXX|idmapping download unmapped download is not coming right
1|GLYG-XXX|if supersearch results is empty, respond with init obj with 0 results
1|GLYG-XXX|go over ignore list for supersearch_init
?|GLYG-XXX|NOR is possible but NAND cannot be done from my side
1|GLYG-XXX|supersearch issue
https://api.tst.glygen.org/supersearch/search?query=[{%22concept%22:%22protein%22,%22query%22:{%22aggregator%22:%22$and%22,%22aggregated_list%22:[],%22unaggregated_list%22:[{%22path%22:%22uniprot_ac%22,%22order%22:0,%22operator%22:%22$eq%22,%22string_value%22:%22P14210%22}]}},{%22concept%22:%22site%22,%22query%22:{%22aggregator%22:%22$and%22,%22aggregated_list%22:[],%22unaggregated_list%22:[{%22path%22:%22start_pos%22,%22order%22:0,%22operator%22:%22$eq%22,%22numeric_value%22:%22294%22},{%22path%22:%22end_pos%22,%22order%22:1,%22operator%22:%22$eq%22,%22numeric_value%22:%22294%22},{%22path%22:%22glycosylation%22,%22order%22:2,%22operator%22:%22$eq%22,%22string_value%22:[]}]}}]
1|GLYG-XXX|idmapping download not working for mapped (see email)
1|GLYG-XXX|Can you please send typeahead field values in super search init api for glycan id, protein id so that we can implement the front end part of type ahead.
1|GLYG-XXX|pages home_init stats duplicated
1|GLYG-XXX|add site_seq to site records
1|GLYG-XXX|make every record have history (introduced date/version)
1|GLYG-XXX| why does G19619KS has "removed" history
1|GLYG-XXX|idmapping to glytoucan and uniprotkb (add these resources in crossref)
1|GLYG-XXX|implement hit_score for site search
1|GLYG-XXX|some site records do not have any site information (all snv, gltcosylation ... lists are empty -- filter out such site records altogether)
1|GLYG-XXX|protein alignment API for isoformset.uniprokb (example accession)
1|GLYG-XXX|data download for orthogs_list and genelocus_list
1|GLYG-XXX|add association flag in supersearch
1|GLYG-XXX|work on collapsed/integratred paths (iteration-4 on the spreadsheet)
1|GLYG-XXX|Talk to Dacian about tst docker issue and performance on dev
1|GLYG-XXX|https://docs.google.com/spreadsheets/d/1fVG14c6EjTqdVcWJlFh4sMxZrgnCXZYKGgjkRAYaL08/edit?usp=sharing  
1|GLYG-XXX|add "enum": ["true", "false"] for the new *_flag fields
1|GLYG-XXX|add "ne" to string values in oplist supersearch_init
1|GLYG-XXX|initial record_count values in supersearch_init are coming zero (fix the bug)
1|GLYG-XXX|id mapping dynamic from-to
1|GLYG-1540|The new download options Raja requested and we discussed yesterday
1|GLYG-1541|Supersearch ticket which information in protein should be queried for disease information
1|GLYG-1546|change max_query_value_len to 10000 (already done)
1|GLYG-1542|supersearch_init max_field_length should be based on data
1|GLYG-XXX|motif list missing synoym values
1|GLYG-XXX|replacor history should have more info talking about replacee (eg. P04439 --> added category type "inherits")
1|GLYG-XXX|replaced by many (e.g Q13065-1 replaced by both P0DSO3-1 and P0DTW1-1)
1|GLYG-XXX|add bylikage to supersearch_init

0|GLYG-XXX|does NOT work for aggregator?
0|GLYG-XXX|add "API analytics" functionality including logs


1|GLYG-XXX|recover disease in expression_disease even when signficance is no
1|GLYG-XXX|enzyme to glycan edge in the supersearch_init also in search
1|GLYG-XXX|when an edge is not disabled, return results for it even if it is empty list_id
1|GLYG-XXX|within bylinkage don't return list_id values for non-listable concepts
1|GLYG-XXX|make bylinkage list API also return result_summary
1|GLYG-XXX|change query structure of of supersearch to take dict instead of list and make ignored_edges to be global, also change direction to have both/single



1|GLYG-XXX|Motif-Glycan bylikage (reverse disabling list_id) on supersearch, supersearch_init and supersearch_list
1|GLYG-XXX|handle direction:single, and make direction to be required, and also do not return numbers for ignored directions
1|GLYG-XXX|field order is not being picked up in supersearch_init
1|GLYG-XXX|make API test page convinient to go to full page view
1|GLYG-XXX|glycan search_init as type/subtype hierachy
1|GLYG-1555|create new site_init API
1|GLYG-XXX|append list of active event list of objects to home_init API ("events" property)
1|GLYG-XXX|make venue optional, add optional URL
1|GLYG-XXX|property names and order (Rahi, Jeet)
1|GLYG-XXX|glycan type/subtype
1|GLYG-XXX|motif synomyms -- separete ";" merged 
1|GLYG-XXX|add _flag to site_init id values


1|GLYG-XXX|make site detail take ac in addition to canonical ac
1|GLYG-XXX|add example IDs in idmapping search init
1|GLYG-XXX|make motif keywords list of objects (label and url --> Rahi produces lookup file)
1|GLYG-XXX|remove phosphorylation_flag and glycation_flag from site_init
1|GLYG-1571|add gene name to homolog objects
1|GLYG-1572|site detail api download
1|GLYG-1567|In usecase init api response predicted and both options are missing 
1|GLYG-1570|Add a download option to download all the rows with “Glycans With This Motif” on the motif detail page, json format is available add csv format
1|GLYG-1547|supersearch_init add field order based on misc/*property_info.csv
1|GLYG-1573|glycan detail enzyme section
1|GLYG-1560|Global search glycan count not matching (use GM2, 4 glycans claimed but only two glycans are in the list)
1|GLYG-1568|Add publication section in global search api results
1|GLYG-1569|concept_query_list should be empoty




0|GLYG-1563|If edge is not disabled and if count is 0 then the bylinkage count should be 0 and the empty list id should be returned.

0|GLYG-1574|super search site bylinkage should have disease count and list id (search for disease = "Alzheimers dementia", site-->bylinkage should have some values)

0|GLYG-XXX|Make sorting systematic