diff --git a/doc/admin/README.md b/doc/admin/README.md index 34c3402d9b6213d404cb7fd1918de5cedf03d9f5..0dfc14db061123f335137c7356ae169669f7b222 100755 --- a/doc/admin/README.md +++ b/doc/admin/README.md @@ -228,7 +228,7 @@ They correspond to different types of stocks. Each type is stored in a specific | Field name | Type | What you enter in this field | | ---------- | ---- | ---------------------------- | | Id | Integer | A unique integer | -| Name | Character string | Plasmid's name (free text). Must be unique | +| Name | Character string | Oligo's name (free text). Must be unique | | Sequence | Character string | The DNA sequence of the oligo, always **5-prime to 3-prime** ! | | Description | Character string | A description of the oligo (free text) | | Author | Character string | The lab member who obtained the oligo. Dropdown selection made from the `name` field of the `users` table | @@ -252,32 +252,148 @@ Clicking the `CopySeq` button copies the full oligo sequence to your clipboard. *[Back to Contents](#Contents)* ### Strains <a name="Strains"></a> -xxx + + +| Field name | Type | What you enter in this field | +| ---------- | ---- | ---------------------------- | +| Id | Integer | A unique integer | +| Name | Character string | Strain's name (free text) | +| Species | Character string | Strain's species. Dropdown selection made from the `name` field of the `species` table. | +| Other names | Character string | Strain's other name. Optionnal | +| General background | Character string | Genetic background of the strain. Dropdown selection made from the `name` field of the `backgrounds` table. | +| Comments | Character string | A description of the strain (free text) | +| Mating type | Character string | Strain's mating type. Dropdown selection made from the `alleles` field of the `st_mats` table. | +| ade2 | Character string | Modifications at ade2 locus. Leave empty if none. Dropdown selection made from the `alleles` field of the `st_ade2s` table. | +| his3 | Character string | Modifications at his3 locus. Leave empty if none. Dropdown selection made from the `alleles` field of the `st_his3s` table. | +| leu2 | Character string | Modifications at leu2 locus. Leave empty if none. Dropdown selection made from the `alleles` field of the `st_leu2s` table. | +| met15 | Character string | Modifications at met15 locus. Leave empty if none. Dropdown selection made from the `alleles` field of the `st_met15s` table. | +| trp1 | Character string | Modifications at trp1 locus. Leave empty if none. Dropdown selection made from the `alleles` field of the `st_trp1s` table. | +| ura3 | Character string | Modifications at ura3 locus. Leave empty if none. Dropdown selection made from the `alleles` field of the `st_ura3s` table. | +| ho | Character string | Modifications at ho locus. Leave empty if none. Freetext | +| locus1 | Character string | Modifications at a locus not mentionned in other fields. Free text | +| locus2 | Character string | Modifications at a locus not mentionned in other fields. Free text | +| locus3 | Character string | Modifications at a locus not mentionned in other fields. Free text | +| locus4 | Character string | Modifications at a locus not mentionned in other fields. Free text | +| locus5 | Character string | Modifications at a locus not mentionned in other fields. Free text | +| Parental strain | Character string | The id of the strain from which this one was obtained. Free text | +| Obtained by | Character string | Method used to obtain the strain. Free text | +| Checkings | Character string | Checkings performed on this strain such as PCR, or microscopy | +| Extrachromosomal plasmid | Character string | Any plamid present in this strain | +| Cytoplasmic character | Character string | Modifications of cytoplasmic contents. Free text. | +| Reference | Character string | Litterature refenrence related to the strain | +| Author | Character string | Person authoring this strain. Dropdown selection made from the `name` field of the `users` table. | +| Relevant plasmids | Character string | Plasmids related to the design of the strain. Free text | +| Relevant oligos | Character string | Oligos related to the design of the strain. Free text | +| Files | Media files | Uploaded media files of any format that you want to be associated with the strain | +| Created at | Timestamp | Timestamp of the record in the database | +| Updated at | Timestamp | Timestamp of updates | +| Warning | Boolean | Option used to signal an issue with the strain | + *[Back to Contents](#Contents)* ### Antibodies <a name="Antibodies"></a> -xxx + + +| Field name | Type | What you enter in this field | +| ---------- | ---- | ---------------------------- | +| Id | Integer | A unique integer | +| Antigen | Character string | Antibody's antigen (free text) | +| Host | Character string | Host of the antibody. Dropdown selection made from the `name` field of the `hosts` table. | +| Supplier | Character string | The company or service who supplied the oligo. Dropdown selection made from the `name` field of the `suppliers` table | +| Type | Character string | Type of antibody. Dropdown selection made from the `name` field of the `xxx` table. | +| Productid | Character string | Supplier's reference of the antibody (free text) | +| Batchid | Character string | Production batch reference (free text) | +| Instock | Character string | Stock status of the antibody. Dropdown selection made from the `name` field of the `xxx` table. | +| Ordered By | Character string | Person who ordered this antibody. Dropdown selection made from the `name` field of the `users` table. | +| Comments | Character string | A description or comment about the antibody (free text) | +| Created At | Timestamp | Timestamp of the record in the database | +| Obtention Date | Timestamp | Date when the antibody was obtained | +| projects | Relationship | Links to projects related to this antibody. Dropdown selection made from the `name` field of the `projects` table | +| Files | Media files | Uploaded media files of any format that you want to be associated with the antibody. | + *[Back to Contents](#Contents)* ### Cell lines <a name="Celllines"></a> -xxx + + +| Field name | Type | What you enter in this field | +| ---------- | ---- | ---------------------------- | +| Id | Integer | A unique integer | +| Name | Character string | Cell line's name (free text) | +| Celltype | Character string | Type of cells. Dropdown selection made from the `name` field of the `cell_types` table. | +| Description | Character string | A description or comments about the cell line (free text) | +| Origin | Character string | Source from which the cell line was obtained (free text) | +| Author | Character string | Person authoring this cell line. Dropdown selection made from the `name` field of the `users` table. | +| Files | Media files | Uploaded media files of any format that you want to be associated with the cell line. | +| Projects | Relationship | Links to projects related to this cell line. Dropdown selection made from the `name` field of the `projects` table | +| Created at | Timestamp | Timestamp of the record in the database | +| Updated at | Timestamp | Timestamp of updates | + + *[Back to Contents](#Contents)* ### Notebooks <a name="Notebooks"></a> -xxx + + +| Field name | Type | What you enter in this field | +| ---------- | ---- | ---------------------------- | +| Id | Integer | A unique integer | +| Serial number | Character string | Reference number of the notebook. (free text) | +| Author | Character string | Author of the notebook. Dropdown selection made from the `name` field of the `users` table. | +| Begin Date | Date | Date at which the notebook was started | +| End Date | Date | Date at which the notebook was ended | +| Created at | Timestamp | Timestamp of the record in the database | +| Updated at | Timestamp | Timestamp of updates | + + *[Back to Contents](#Contents)* ### Pipets <a name="Pipets"></a> -xxx + + + +| Field name | Type | What you enter in this field | +| ---------- | ---- | ---------------------------- | +| Id | Integer | A unique integer | +| Serial number | Character string | Reference number of the pipet. (free text) | +| Brand | Character string | Pipet's brand. Dropdown selection made from the `name` field of the `suppliers` table. | +| Type | Character string | Pipet's type such as volume of number of channels. Dropdown selection made from the `name` field of the `pipet_types` table. | +| Files | Media Files | Uploaded media files of any format that you want to be associated with the pipet. | +| History | Character string | xxx | +| Created at | Timestamp | Timestamp of the record in the database | +| Updated at | Timestamp | Timestamp of updates | + + + *[Back to Contents](#Contents)* ### Well plates <a name="Wellplates"></a> -xxx + + + +| Field name | Type | What you enter in this field | +| ---------- | ---- | ---------------------------- | +| Id | Integer | A unique integer | +| Format | Character string | Plate's format (free text) | +| Name | Character string | Plate's name (free text) | +| Author | Character string | Person authoring this wellplate. Dropdown selection made from the `name` field of the `users` table. | +| Content Type | Character string | Plate's content (free text) | +| Thawings | Integer | Number of times the plate was thawed | +| Freeze Date | Date | Date at which the plate was frozen | +| Files | Media Files | Uploaded media files of any format that you want to be associated with the plate. | +| Freezer Id | Integer | Freezer in which the plate is kept | +| Comments | Character string | Comments or description about the weelplate (free text) | +| Warning | Boolean | Option used to signal an issue with the plate | +| Created at | Timestamp | Timestamp of the record in the database | +| Updated at | Timestamp | Timestamp of updates | + + + *[Back to Contents](#Contents)* @@ -328,7 +444,7 @@ They correspond to pieces of information that are linked to stocks. Each type of | Name | Character string | Feature's name (free text) | | Comments | Character string | Free text giving comments on the feature | | Created At | Timestamp | Timestamp of the record creation in the database | -| Created At | Timestamp | Timestamp of the record update in the database | +| Updated At | Timestamp | Timestamp of the record update in the database | | Color | Character string | The color with which the feature will be displayed on plasmid maps. Do **NOT** edit directly because your color name or syntax may not be recognized properly. Instead, select one of those proposed by the dropdown menu | After adding or editing DNA features entries, your **modifications will NOT directly appear on the plasmid maps** unless you intentionally **update plasmid maps with the latest features**. Technically, this corresponds to updating the BLAST database containing the DNA features sequences. To achieve this update, go to the `browse` page of the `DNA features` and click on the blue button (top right) labeled `Update Plasmid Maps with these Features`. @@ -339,25 +455,58 @@ Now your latest changes should appear on the [plasmid maps](#Plasmidmaps). ### Events <a name="Events"></a> -xxx + +| Field name | Type | What you enter in this field | +| ---------- | ---- | ---------------------------- | +| Id | Integer | A unique integer | +| Datatype | Character string | Type of data | +| Event date | Date | Date of the event | +| Event type | Character string | Type of event | +| Description | Character string | A description of the event. (free text) | +| Files | Media | Any media you may want to upload regarding the event | +| Created At | Timestamp | Timestamp of the record creation in the database | +| Updated At | Timestamp | Timestamp of the record update in the database | + + *[Back to Contents](#Contents)* ### Passages <a name="Passages"></a> -xxx +| Field name | Type | What you enter in this field | +| ---------- | ---- | ---------------------------- | +| Id | Integer | A unique integer | +| Cell line | Character string | The cell line this passage is about | +| Name | Character string | Passage's name (free text) | +| Author | Character string | Author of the passage. Dropdown selection made from the `name` field of the `users` table. | +| Freezing Date | Timestamp | Date when the passage was frozen | +| Created At | Timestamp | Timestamp of the record creation in the database | +| Updated At | Timestamp | Timestamp of the record update in the database | + *[Back to Contents](#Contents)* ### Species <a name="Species"></a> -xxx +| Field name | Type | What you enter in this field | +| ---------- | ---- | ---------------------------- | +| Id | Integer | A unique integer | +| Name | Character string | Specie's name (free text). Must be unique, will appear in dropdown selections. | +| Created At | Timestamp | Timestamp of the record creation in the database | +| Updated At | Timestamp | Timestamp of the record update in the database | + *[Back to Contents](#Contents)* ### Suppliers <a name="Suppliers"></a> -xxx +| Field name | Type | What you enter in this field | +| ---------- | ---- | ---------------------------- | +| Id | Integer | A unique integer | +| Name | Character string | Supplier's name (free text). Must be unique, will appear in dropdown selections. | +| Created At | Timestamp | Timestamp of the record creation in the database | +| Updated At | Timestamp | Timestamp of the record update in the database | + *[Back to Contents](#Contents)* ### Storage locations <a name="Storage"></a> @@ -418,7 +567,17 @@ For your information, boxpositions are referenced by the id of the box, and by t ### Projects <a name="Projects"></a> -xxx +| Field name | Type | What you enter in this field | +| ---------- | ---- | ---------------------------- | +| Id | Integer | A unique integer | +| Name | Character string | Project's name (free text). Must be unique, will appear in dropdown selections. | +| Leader | Character string | Leader of the project. Dropdown selection made from the `name` field of the `users` table. | +| Files | Media | Any media you may want to upload regarding the event | +| Status | Character string | Project's status. | +| Description | Character string | A description of the project. (free text) | +| Created At | Timestamp | Timestamp of the record creation in the database | +| Updated At | Timestamp | Timestamp of the record update in the database | + *[Back to Contents](#Contents)*