{"id":215,"date":"2022-07-18T12:38:29","date_gmt":"2022-07-18T11:38:29","guid":{"rendered":"https:\/\/insdc.org\/?page_id=215"},"modified":"2024-08-19T15:22:36","modified_gmt":"2024-08-19T14:22:36","slug":"missing-value-reporting","status":"publish","type":"page","link":"https:\/\/www.insdc.org\/technical-specifications\/missing-value-reporting\/","title":{"rendered":"Missing Value Reporting"},"content":{"rendered":"<p>The International Nucleotide Database Collaboration (INSDC) have a standardised missing\/null value reporting language to be used where a value of an expected format for sample metadata reporting<strong> can not<\/strong> be provided.<\/p>\n<p>The controlled vocabulary takes into account different type of constraints. Submitters are <strong>strongly<\/strong> encouraged to always provide true values. However, if missing\/null value reporting is required, submitters are asked to use a term with the finest granularity for their situation. See the table below for accepted missing value reporting terms.<\/p>\n<p><strong>INSDC Missing Value Reporting Terms:<\/strong><\/p>\n<table class=\"insdc-table vf-table\">\n<thead class=\"vf-table__header\">\n<tr class=\"vf-table__row\">\n<th class=\"vf-table__heading\">INSDC term (top level)<\/th>\n<th class=\"vf-table__heading\">INSDC term (lower level)<\/th>\n<th class=\"vf-table__heading\">Definition<\/th>\n<th class=\"vf-table__heading\">INSDC term (reporting level)<\/th>\n<th class=\"vf-table__heading\">Definition<\/th>\n<\/tr>\n<\/thead>\n<tbody class=\"vf-table__body\">\n<tr class=\"vf-table__row\">\n<td class=\"centered vf-table__cell\" rowspan=\"2\">not applicable<\/td>\n<td class=\"row-header centered vf-table__cell\" rowspan=\"2\"><\/td>\n<td class=\"vf-table__cell\" rowspan=\"2\">Information is inappropriate to report, can\u00a0indicate that the standard itself fails to\u00a0model or represent the information\u00a0appropriately<\/td>\n<td class=\"row-header centered vf-table__cell\">control sample<\/td>\n<td class=\"vf-table__cell\">Information is not applicable as the sample represents a negative control sample collected in a lab.<\/td>\n<\/tr>\n<tr class=\"vf-table__row\">\n<td class=\"row-header centered vf-table__cell\">sample group<\/td>\n<td class=\"vf-table__cell\">Information is not applicable as the sample represents a group of samples that do not have a single origin. E.g. for co-assembly or transcriptome assembly.<\/td>\n<\/tr>\n<tr class=\"vf-table__row\">\n<td class=\"centered vf-table__cell\" rowspan=\"6\">missing<\/td>\n<td class=\"row-header centered vf-table__cell\" rowspan=\"3\">not collected<\/td>\n<td class=\"vf-table__cell\" rowspan=\"3\">Information of an expected format was not given because it has not been collected<\/td>\n<td class=\"row-header centered vf-table__cell\">synthetic construct<\/td>\n<td class=\"vf-table__cell\">Information does not exist as the sample represents an ab-initio synthetic construct.<\/td>\n<\/tr>\n<tr class=\"vf-table__row\">\n<td class=\"row-header centered vf-table__cell\">lab stock<\/td>\n<td class=\"vf-table__cell\">Information was not collected as the sample represents a cultured cell line or model organism under long-term lab control.<\/td>\n<\/tr>\n<tr class=\"vf-table__row\">\n<td class=\"row-header centered vf-table__cell\">third party data<\/td>\n<td class=\"vf-table__cell\">Information does not exist as the metadata was not collected or reported in records predating the 2023 agreement. For use in Third PArty data submissions.<\/td>\n<\/tr>\n<tr class=\"vf-table__row\">\n<td class=\"row-header centered vf-table__cell\">not provided<\/td>\n<td class=\"vf-table__cell\">Information of an expected format was not given, a value may be given at the later stage<\/td>\n<td class=\"row-header centered vf-table__cell\">data agreement established pre-2023<\/td>\n<td class=\"vf-table__cell\">Data agreements were established before the 2023 INSDC standard and metadata can not be provided. A value may be given at a later stage.<\/td>\n<\/tr>\n<tr class=\"vf-table__row\">\n<td class=\"row-header centered vf-table__cell\" rowspan=\"2\">restricted access<\/td>\n<td class=\"vf-table__cell\" rowspan=\"2\">Information exists but can not be released openly because of privacy concerns<\/td>\n<td class=\"row-header centered vf-table__cell\">endangered species<\/td>\n<td class=\"vf-table__cell\">Information can not be reported as the target organism is endangered e.g. on the IUCN red-list.<\/td>\n<\/tr>\n<tr class=\"vf-table__row\">\n<td class=\"row-header centered vf-table__cell\">human-identifiable<\/td>\n<td class=\"vf-table__cell\">Information can not be reported as the metadata would make the sample human-identifiable.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><strong>Usage of INSDC Missing Value Reporting Terms:<\/strong><\/p>\n<p>Please use the above standardised missing value vocabulary <strong>only if a true value of an expected format for a mandatory field is missing<\/strong>. If a true value is missing for a <strong>recommended<\/strong> or an <strong>optional<\/strong> field, then these fields should not be used for reporting at all. When reporting a missing mandatory field, the eight granular \u2018<strong>reporting level<\/strong>\u2019 terms need to be preceded with the term \u2018<strong>missing:<\/strong> \u2019 to declare both the absence of a true value as well as the reason.<\/p>\n<p>Example of usage:<\/p>\n<p><strong>geographic location (country and\/or sea)<\/strong>: missing: data agreement-established pre-2023<\/p>\n<p><strong>collection date<\/strong>: missing: control sample<\/p>\n<p><strong>geographic location (country and\/or sea)<\/strong>: missing: human-identifiable<\/p>\n","protected":false},"excerpt":{"rendered":"<p>The International Nucleotide Database Collaboration (INSDC) have a standardised missing\/null value reporting language to be used where a value of an expected format for sample metadata reporting can not be provided. The controlled vocabulary takes into account different type of constraints.…<\/p>\n","protected":false},"author":2,"featured_media":0,"parent":437,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"acf":[],"_links":{"self":[{"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/pages\/215"}],"collection":[{"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/comments?post=215"}],"version-history":[{"count":4,"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/pages\/215\/revisions"}],"predecessor-version":[{"id":637,"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/pages\/215\/revisions\/637"}],"up":[{"embeddable":true,"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/pages\/437"}],"wp:attachment":[{"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/media?parent=215"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}