diff --git a/content/coll_manager/citation/_index.md b/content/coll_manager/citation/_index.md index d4410dcb..10e5c0a2 100644 --- a/content/coll_manager/citation/_index.md +++ b/content/coll_manager/citation/_index.md @@ -1,7 +1,9 @@ --- title: "Data Citations" date: 2022-10-26 +lastmod: 2025-01-31 authors: ["Lindsay Walker"] +editors: ["Katie Pearson"] draft: "false" weight: 24 keywords: ["citations","gbif","data publishing"] @@ -63,7 +65,7 @@ Example CITEME.txt content: > For more information on citation formats, please see the following page: https://serv.biokic.asu.edu/ecdysis/includes/usagepolicy.php ## Data Usage Policy & Portal Citations -Some portal communities maintain their own portal-wide data usage policies for media and specimen records, which includes a recommended citation format for the portal. This information can typically be found on the **_Sitemap_ > _Image Library_ > _Usage Policy and Copyright Information_**. To request modifications to your portal's data usage policy, or to have one added to your portal, contact your portal manager. +Some portal communities maintain their own portal-wide data usage policies for media and specimen records, which includes a recommended citation format for the portal. This information can typically be found on the **_Sitemap_ > _Media Library_ > _Usage Policy and Copyright Information_**. To request modifications to your portal's data usage policy, or to have one added to your portal, contact your portal manager. diff --git a/content/coll_manager/delete/_index.en.md b/content/coll_manager/delete/_index.en.md index fc738ace..c9e3b548 100644 --- a/content/coll_manager/delete/_index.en.md +++ b/content/coll_manager/delete/_index.en.md @@ -1,11 +1,11 @@ --- title: "Deleting Records" date: 2021-12-08 -lastmod: 2024-04-30 +lastmod: 2025-01-31 draft: false weight: 60 authors: ["Katie Pearson"] -editors: ["Lindsay Walker"] +editors: ["Lindsay Walker","Katie Pearson"] keywords: ["delete","remove"] --- @@ -20,7 +20,7 @@ Deleting a specimen record is only appropriate when that specimen no longer exis To delete a record: 1) Navigate to the specimen record that you would like to delete and open the Occurrence Editor form for that record. (See [this page](https://biokic.github.io/symbiota-docs/editor/edit/) for help navigating to specific records.) 2) Open the Admin tab. -3) Select the “Evaluate record for deletion” button to determine whether the record can be safely deleted. If an image is associated with the record, you will need to disassociate the image from the specimen record before it can be deleted (see the [deleting/remapping images page](https://biokic.github.io/symbiota-docs/editor/images/delete/)). Likewise, a warning will appear if the specimen record is linked to a checklist, which must be resolved before the specimen record can be deleted. If there are no warnings at this point, click the "Delete Occurrence" button to remove the record from your dataset. +3) Select the “Evaluate record for deletion” button to determine whether the record can be safely deleted. If an media resource (e.g., image) is associated with the record, you will need to disassociate the resource from the specimen record before it can be deleted (see the [deleting/remapping images page](https://biokic.github.io/symbiota-docs/editor/images/delete/)). Likewise, a warning will appear if the specimen record is linked to a checklist, which must be resolved before the specimen record can be deleted. If there are no warnings at this point, click the "Delete Occurrence" button to remove the record from your dataset. ![Admin tab of the Occurrence Editor](/symbiota-docs/images/admintab_delete.png) diff --git a/content/coll_manager/download/_index.en.md b/content/coll_manager/download/_index.en.md index 9a79c4db..d9e028f5 100644 --- a/content/coll_manager/download/_index.en.md +++ b/content/coll_manager/download/_index.en.md @@ -1,7 +1,7 @@ --- title: "Downloading a Copy of your Database" date: 2021-11-29 -lastmod: 2024-04-30 +lastmod: 2025-01-31 draft: false weight: 55 authors: ["Katie Pearson"] @@ -10,7 +10,7 @@ keywords: ["download", "backup"] --- {{< notice info >}} - This page describes how to download a copy of your data, including occurrence records, determinations, images (as links only), and any other extensions enabled in your portal (e.g., attribute data). It is strongly recommended that curators or collection managers regularly download and internally archive a backup data file in case of emergency. **Doing so is quick and easy**. + This page describes how to download a copy of your data, including occurrence records, determinations, media resources (as links only), and any other extensions enabled in your portal (e.g., attribute data). It is strongly recommended that curators or collection managers regularly download and internally archive a backup data file in case of emergency. **Doing so is quick and easy**. {{}} {{< notice note >}} diff --git a/content/coll_manager/download/exporter/_index.en.md b/content/coll_manager/download/exporter/_index.en.md index 777ec120..db78b891 100644 --- a/content/coll_manager/download/exporter/_index.en.md +++ b/content/coll_manager/download/exporter/_index.en.md @@ -1,6 +1,7 @@ --- title: "Download a Subset of Data (Exporter)" date: 2021-12-07 +lastmod: 2025-01-31 draft: false authors: ["Katie Pearson"] keywords: ["download","exporter"] @@ -13,7 +14,7 @@ keywords: ["download","exporter"] 1. Navigate to your Administration Control Panel (My Profile > Occurrence Managment > name of collection). 2. Click Processing Tools. 3. Click the Exporter tab. -4. Use the Processing Status and additional filters to define the dataset you would like to download from your collection. You can also select whether you would like to download a strict Darwin Core Archive (Darwin Core) or an archive containing all Symbiota fields (Symbiota Native); whether you would like to determination history (identifications), images, and/or occurrence attributes (if enabled); whether you would like the results in a ZIP file; and the file format and character set ([ISO-8859-1](https://en.wikipedia.org/wiki/ISO/IEC_8859-1) or [UTF-8](https://en.wikipedia.org/wiki/UTF-8)) for your download. +4. Use the Processing Status and additional filters to define the dataset you would like to download from your collection. You can also select whether you would like to download a strict Darwin Core Archive (Darwin Core) or an archive containing all Symbiota fields (Symbiota Native); whether you would like to determination history (identifications), multimedia (i.e., links to images), and/or occurrence attributes (if enabled); whether you would like the results in a ZIP file; and the file format and character set ([ISO-8859-1](https://en.wikipedia.org/wiki/ISO/IEC_8859-1) or [UTF-8](https://en.wikipedia.org/wiki/UTF-8)) for your download. 5. Click the Download Records button. ![Exporter Tool](/symbiota-docs/images/exportertool.PNG) diff --git a/content/coll_manager/images/_index.en.md b/content/coll_manager/images/_index.en.md index b4f30b90..40dca444 100644 --- a/content/coll_manager/images/_index.en.md +++ b/content/coll_manager/images/_index.en.md @@ -1,38 +1,46 @@ --- -title: "Images" +title: "Images & Other Media" date: 2021-10-06 -lastmod: 2024-03-19 +lastmod: 2025-01-31 weight: 80 draft: false authors: ["Ed Gilbert","Katie Pearson"] editors: ["Katie Pearson", "Lindsay Walker"] -keywords: ["images"] +keywords: ["images","media"] --- {{< notice info >}} - This page describes the types of images that are available through Symbiota portals. + This page describes the types of media that are supported by Symbiota portals. {{}} -Images may be associated with records in Symbiota portals by storing links to those images in the database tables. If a Symbiota portal is configured to accept images (i.e., image storage at the institution that hosts the portal is allowed), those image links may be generated by the portal. Storage of a large number of images on servers associated with a Symbiota portal (e.g., at Arizona State University) may require an image-hosting agreement and/or incur image-hosting costs. Check with the portal administrator for more information about your portal's image hosting allowances. Otherwise, tools are available to link external URLs to occurrences by matching on catalog numbers. +{{< notice tip >}} + As of Symbiota version 3.2, Symbiota portals support audio files! For this reason, most tools are now labeled **media** or **multimedia** tools, rather than "image tools," as in previous versions of Symbiota. **Media** refers to any audiovisual media such as images or audio files; however, video files are not currently supported. +{{}} + +Media resources may be associated with records in Symbiota portals by storing links to those resources in the database tables. If a Symbiota portal is configured to accept media resources (i.e., media asset storage at the institution that hosts the portal is allowed), those media links may be generated by the portal. Storage of a large number of media resources on servers associated with a Symbiota portal (e.g., at Arizona State University) may require an media-hosting agreement and/or incur media-hosting costs. Check with the portal administrator for more information about your portal's image hosting allowances. Otherwise, tools are available to link external URLs to occurrences by matching on catalog numbers. + +{{< notice note >}} + If your portal is hosted by the [Symbiota Support Hub](https://symbiota.org/symbiota-portals/), you may be eligible for a certain level of media hosting free of charge. Contact [help@symbiota.org](mailto:help@symbiota.org) for more information. +{{}} -There are three categories of images that can be linked to a Symbiota portal: +There are three categories of media that can be linked to a Symbiota portal: {{< tabs >}} - {{< tab "Occurrence (Specimen) Images" >}} - Images of physical specimens should be linked to their respective specimen records. Specimen images are available both from the Occurrence Details page and the Taxon Profile page for the taxon associated with the most recent determination. If the specimen identification is annotated, the identification of the image will be automatically re-mapped to that taxon. Specimen images can be added through the Occurrence Editor or in batch via multiple processes. + {{< tab "Occurrence (Specimen) Media" >}} + Media (e.g., images) relating to physical specimens should be linked to their respective specimen records. Specimen-linked media are available both from the Occurrence Details page and the Taxon Profile page for the taxon associated with the most recent determination. If the specimen identification is annotated, the taxonomic identification of the media resource will be automatically re-mapped to that taxon. Specimen-linked media can be added through the Occurrence Editor or in batch via multiple processes.

- See Uploading Images for more details. + See Uploading Images & Other Media for more details. {{}} - {{< tab "Field Images without Location" >}} - Images without specific locality information (e.g. lat/long coordinates) are linked only to the scientific name of the organism. These images can be viewed through Taxon Profile Pages, which have general information such as descriptions, distribution maps, synonyms, and common names. Field images are uploaded and managed through the Taxon Profile pages by users with Taxon Profile editing permissions. Field images with specific locality details (e.g. coordinates) can be loaded as Image Vouchers (see "Field Images with Location" tab). See Uploading Images for more details. + {{< tab "Field Media without Location" >}} + Media without specific locality information (e.g. lat/long coordinates) are linked only to the scientific name of the organism. These media resources can be viewed through Taxon Profile Pages, which have general information such as descriptions, distribution maps, synonyms, and common names. Field media are uploaded and managed through the Taxon Profile pages by users with Taxon Profile editing permissions. Field media with specific locality details (e.g. coordinates) can be loaded as Media Vouchers (see "Field Media with Location" tab). See Uploading Images & Other Media for more details. {{}} - {{< tab "Field Images with Location" >}} - Field images with specific locality information can adequately serve as vouchers for field observations of many birds, mammals, and easy-to-identify plants. In some instances, they may actually be preferable, for instance if the organism is rare or the observer does not have the appropriate collecting permit. These images are similar to georeferenced specimen records in that they are searchable occurrence records that place a dot on the species distribution maps. There are, however, some taxonomic groups that typically require microscopic or chemical analysis for accurate identification (e.g. lichens, bryophytes, fungi). For such organisms, field images will have limited value. For this reason, some data portals might not allow the submission of observations without a physical specimen. + {{< tab "Field Media with Location" >}} + Field media with specific locality information can adequately serve as vouchers for field observations of many birds, mammals, and easy-to-identify plants. In some instances, they may actually be preferable, for instance if the organism is rare or the observer does not have the appropriate collecting permit. These media resources are similar to georeferenced specimen records in that they are searchable occurrence records that place a dot on the species distribution maps. There are, however, some taxonomic groups that typically require microscopic or chemical analysis for accurate identification (e.g. lichens, bryophytes, fungi). For such organisms, field images will have limited value. For this reason, some data portals might not allow the submission of observations without a physical specimen.

Image Vouchers are displayed on both the Occurrence Details and the Taxon Profile pages. Image-supported observations can be uploaded using the Observation Submission page. Up to three images can be submitted for a single observation. Data fields required for an image to qualify as a voucher include: observer name, observation date, country, state, locality description, latitude, longitude, and at least one image. Contact your data portal administrator for information on whether observations are allowed and the necessary protocols for submitting an observation. Some portals require the review of a tutorial before one is authorized to submit an observation. - See Uploading Images for more details. + See Uploading Images & Other Media for more details. {{}} {{}} diff --git a/content/coll_manager/images/batch/_index.en.md b/content/coll_manager/images/batch/_index.en.md index cae95055..65b1e5f9 100644 --- a/content/coll_manager/images/batch/_index.en.md +++ b/content/coll_manager/images/batch/_index.en.md @@ -1,7 +1,7 @@ --- -title: "Batch Uploading/Linking Images" +title: "Batch Adding Images/Media" date: 2021-10-06 -modified: 2023-12-06 +modified: 2025-01-31 weight: 1 authors: ["Ed Gilbert","Katie Pearson"] editors: ["Katie Pearson"] @@ -9,25 +9,25 @@ keywords: ["images"] --- {{< notice info >}} - This page describes general workflows for adding multiple images to a portal at one time. Technically, images are not stored within a Symbiota database. Instead, the URLs of the images are mapped to specimen records. Contact the portal manager to inquire about the workflows supported by a given portal. + This page describes general workflows for adding multiple media resources (e.g., images) to a portal at one time. Media resources are not stored within a Symbiota database. Instead, the URLs of the media resources are mapped to specimen records. Contact the portal manager to inquire about the workflows supported by a given portal. {{}} -Images associated with records in a Symbiota portal may be **Externally Hosted** or **Internally Hosted**. +Media resources (e.g., images) associated with records in a Symbiota portal may be **Externally Hosted** or **Internally Hosted**. -* **Externally Hosted** images are those stored on servers that are unrelated to the Symbiota portal (e.g., are housed at another institution). These external servers provide image links, which can then be loaded into the Symbiota database. +* **Externally Hosted** media resources are those stored on servers that are unrelated to the Symbiota portal (e.g., are housed at another institution). These external servers provide media links, which can then be loaded into the Symbiota database. -* **Internally Hosted** images are those stored on servers that are write-accessible to the Symbiota portal server. For example, if you coordinate with Arizona State University to batch upload images to one of their hosted portals (e.g., SEINet, Bryophyte Portal), your images are Internally Hosted. +* **Internally Hosted** media resources are those stored on servers that are write-accessible to the Symbiota portal server. For example, if you coordinate with the Symbiota Support Hub to batch upload images to one of their hosted portals (e.g., SEINet, Bryophyte Portal), your images are Internally Hosted. {{< notice tip >}} Images uploaded or linked to specimens in a Symbiota portal should be JPGs or in another web-friendly format. It is recommended that individual files are no larger than 8 MB to allow users with slower connectivity to view them within a reasonable timeframe. {{}} -#### Batch Adding Externally Hosted Images +#### Batch Adding Externally Hosted Media Resources -Externally Hosted images can be added to Symbiota records using one of three primary methods: (1) using the URL mapping tool and a spreadsheet of catalog numbers with image URLs (documentation coming soon!); (2) mapping a column of image links to the associatedMedia field when conducting a Full Text File Upload or Skeletal File Upload. For more information about uploading text files, see this page. If you already have data in the portal, and you just want to add image links, do NOT use Full Text File Upload; or (3) importing a Darwin Core Archive of your data with a fully-populated multimedia extension. +Externally Hosted media resources can be added to Symbiota records using one of three primary methods: (1) using the URL mapping tool and a [spreadsheet of catalog numbers with media URLs](/symbiota-docs/coll_manager/images/url_upload/); (2) mapping a column of media links to the associatedMedia field when conducting a Full Text File Upload or Skeletal File Upload. For more information about uploading text files, see [this page](/symbiota-docs/coll_manager/upload/). (If you already have data in the portal, and you just want to add media links, do NOT use Full Text File Upload); or (3) importing a Darwin Core Archive of your data with a fully-populated multimedia extension. -#### Batch Adding Internally Hosted Images +#### Batch Adding Internally Hosted Media Resources -There are several workflows used to batch upload/link internally hosted specimen images. Batch processing typically consists of two separate steps: (1) Loading images onto a web server, and (2) Mapping image URLs to Symbiota occurrence records. Step (2) is possible when images are named according to the catalog number or other catalog number associated with the record in the portal. +There are several workflows used to batch upload/link internally hosted specimen media resources. Batch processing typically consists of two separate steps: (1) Loading media resources onto a web server, and (2) Mapping image URLs to Symbiota occurrence records. Step (2) is possible when media resources are named according to the catalog number or other catalog number associated with the record in the portal. -Storage of a large number of images on servers associated with a Symbiota portal may require an image-hosting agreement and/or incur image-hosting costs. Check with the portal administrator for more information about your portal's image hosting allowances and workflows. For ASU-hosted servers, contact the Symbiota Support Hub (help@symbiota.org). \ No newline at end of file +Storage of a large number of images or other media resources on servers associated with a Symbiota portal may require an image-hosting agreement and/or incur image-hosting costs. Check with the portal administrator for more information about your portal's image hosting allowances and workflows. For SSH-hosted servers, contact the Symbiota Support Hub (help@symbiota.org). diff --git a/content/coll_manager/images/url_upload/_index.en.md b/content/coll_manager/images/url_upload/_index.en.md index 5f476e6b..0640b640 100644 --- a/content/coll_manager/images/url_upload/_index.en.md +++ b/content/coll_manager/images/url_upload/_index.en.md @@ -1,62 +1,62 @@ --- -title: "Image URL Upload" +title: "Image/Media URL Upload" date: 2023-10-31 -lastmod: 2024-08-08 +lastmod: 2025-01-31 weight: 10 authors: ["Katie Pearson"] editors: ["Lindsay Walker"] -keywords: ["images"] +keywords: ["images","media","audio"] --- {{< notice info >}} - This page describes how to associate externally hosted images with records in your portal using a CSV of image links/URLs. + This page describes how to associate externally hosted media resources (e.g., images) with records in your portal using a CSV of links/URLs. {{}} -### Adding Images via URLs +### Adding Media Resources via URLs 1. Navigate to your Administration Control Panel (My Profile > Occurrence Management > name of your collection). 2. Click Import/Update Specimen Records, then select "Extended Data Import". 3. Click the "Choose File" button to upload a properly formatted associations file into the uploader (see sections below for formatting requirements). - 4. Select "Image Field Map" from the Import Type dropdown menu. + 4. Select "Media Field Map" from the Import Type dropdown menu. 5. Click the "Initialize Import" button. - 6. Map the fields in your input file (shown on the left) to appropriate target fields (see table below). - 7. If you would like to create a new record for each identifier that does not match an existing identifier in the system, check the box labeled "Link image to new blank record if catalog number does not exist." - 8. Click the Import Data button. + 6. Select the [**format**](https://ac.tdwg.org/format/) for your media item from the dropdown list. Note that only one type of format may be uploaded at a time. + 7. Map the fields in your input file (shown on the left) to appropriate target fields (see table below). + 8. If you would like to create a new record for each identifier that does not match an existing identifier in the system, check the box labeled "Link media to new blank record if catalog number does not exist." + 9. Click the Import Data button. {{< notice tip >}} - ⚠️ When providing images via URLs, the URLs should begin with "**https://**" (not "http://") in order for them to display correctly in various browsers. This is especially important for thumbnail images. If you provide images using URLs containing "https" and they do not display correctly in your Symbiota portal, check that the server that hosts your images maintains an SSL certificate that supports the use of "https". + ⚠️ When providing media resources via URLs, the URLs should begin with "**https://**" (not "http://") in order for them to display correctly in various browsers. This is especially important for thumbnail images. If you provide media links using URLs containing "https" and they do not display correctly in your Symbiota portal, check that the server that hosts your media resources maintains an SSL certificate that supports the use of "https". {{}} -### Setting Up an Image Import File +### Setting Up a Media Import File A template for this upload type can be found [here](https://biokic.github.io/symbiota-docs/documents/GeneralResourceUploadTemplate.xlsx). -The required fields for this upload type are (1) a subject identifier for the occurrence you are linking to (occurrenceID, catalog number, and/or other catalog number), and (2) originalUrl. The originalUrl should include **a direct link to the desired image** (i.e., ideally ending in .jpg or .tif or some other image file extension). Note that uploading a link to a webpage where that image may be found rather than directly to the image may result in images not displaying as expected. +The required fields for this upload type are (1) a subject identifier for the occurrence you are linking to (occurrenceID, catalog number, and/or other catalog number), and (2) originalUrl. The originalUrl should include **a direct link to the desired media resource** (i.e., ideally ending in .jpg or .tif or some other media file extension). Note that uploading a link to a webpage where that media resource may be found (e.g., YouTube) rather than directly to the media resource may result in media not displaying as expected. -Optional fields are listed in the table below. +Optional fields are included in the table below. -### Image Url Mapping Fields +### Media Url Mapping Fields | Field Name | Data Type (Length in characters) | Description | |--------------------------------|------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| subject identifier: [**catalogNumber**](https://dwc.tdwg.org/terms/#dwc:catalogNumber) | Text (32) | The primary human-readable identifier for the record you are linking the image to. | -| subject identifier: [**otherCatalogNumbers**](https://dwc.tdwg.org/terms/#dwc:otherCatalogNumbers) | Text (45) | An alternative catalog number stored as an "Additional Identifier" in the portal for the record you are linking the image to. See [this page](https://biokic.github.io/symbiota-docs/editor/edit/fields/catno/) for more context. | -| subject identifier: [**occurrenceID**](https://dwc.tdwg.org/terms/#dwc:occurrenceID) | Text (255) | The global unique identifier (GUID) of the record you are linking the image to. | +| subject identifier: [**catalogNumber**](https://dwc.tdwg.org/terms/#dwc:catalogNumber) | Text (32) | The primary human-readable identifier for the record you are linking the media resource to. | +| subject identifier: [**otherCatalogNumbers**](https://dwc.tdwg.org/terms/#dwc:otherCatalogNumbers) | Text (45) | An alternative catalog number stored as an "Additional Identifier" in the portal for the record you are linking the media resource to. See [this page](https://biokic.github.io/symbiota-docs/editor/edit/fields/catno/) for more context. | +| subject identifier: [**occurrenceID**](https://dwc.tdwg.org/terms/#dwc:occurrenceID) | Text (255) | The global unique identifier (GUID) of the record you are linking the media resource to. | | [**accessRights**](https://dwc.tdwg.org/terms/#dcterms:accessRights) | Text (255) | A url to the page describing who can access the resource or an indication of its security status.| -| anatomy | Text (100) | Textual description of the anatomical features visible in the image or media item. | -| archiveurl | Text (255) | A stable link to a publicly available archival image (generally a large TIF or RAW file). Not commonly used. | -| caption | Text (100) | A textual description of the image or media item. The caption will be publicly viewable and should ideally be kept brief.| +| anatomy | Text (100) | Textual description of the anatomical features visible in the media resource. | +| archiveurl | Text (255) | A stable link to a publicly available archival media resource (generally a large TIF or RAW file). Not commonly used. | +| caption | Text (100) | A textual description of the media resource. The caption will be publicly viewable and should ideally be kept brief.| | copyright | Text (255) | The organization to which a copyright or license belongs. | -| [**format**](https://ac.tdwg.org/format/) | Text (100) | The media type of the media item, such a JPG, TIFF, video, GIF, etc.| | hashFunction | Text (45) | Name of the function that was used to generate a hash (fixed-size value representation of the item) for the media item. See [this article](https://en.wikipedia.org/wiki/Hash_function) for more information about hashing.| | hashValue | Text (45) | A fixed-size value representation of the media item generated using a given hashing algorithm. See [this article](https://en.wikipedia.org/wiki/Hash_function) for more information about hashing.| -| mediaMD5 | Text (45) | Hash for the image or media item created using the MD5 algorithm. See [this article](https://en.wikipedia.org/wiki/Hash_function) for more information about hashing.| -| notes | Text (350) | Comments or other notes regarding the image or media item.| -| originalUrl | Text (255) | The large or highest-quality version of the image or media item. This url will be used to create thumbnail and web-ready versions of images using the thumbnail maintenance tool, if used. | -| [**owner**](http://ns.adobe.com/xap/1.0/rights/Owner) | Text (250) | The legal owner of the image or media item. | -| photographer | Text (100) | The creator of the image or media item. | -| photographerUid | Integer (10) | The unique number assigned to the Symbiota portal user who created the image or media item. Note that this can only be populated in cases when the photographer has a user account in the portal. | -| referenceUrl | Text (255) | A link to a URL or page that features the image in the original software. | -| [**rights**](http://dublincore.org/usage/terms/history/#rightsT-001) | Text (255) | The rights applied to the image or media item dictating appropriate reuse of the item. For example, a [Creative Commons license](https://creativecommons.org/share-your-work/cclicenses/) may be applied here.| -| sortOccurrence | Integer (11) | The sort order of the image as it will appear on the page related to the occurrence record. Lower numbers will be displayed before higher numbers.| -| sourceIdentifier | Text (150) | A unique identifier belonging to the image or media item provided by the source of the media item. | -| thumbnailUrl | Text (255) | A thumbnail-sized version (e.g., ~300 pixels in the widest dimension) of the image or media item to be shown quickly in search results.| -| url | Text (255) | A web-ready version of the image or media item, such as a JPG no larger than 2 MB. This is the version that is displayed as "medium resolution" in the occurrence editor.| +| mediaMD5 | Text (45) | Hash for the media resource created using the MD5 algorithm. See [this article](https://en.wikipedia.org/wiki/Hash_function) for more information about hashing.| +| notes | Text (350) | Comments or other notes regarding the media resource.| +| originalUrl | Text (255) | The large or highest-quality version of the media resource. This url will be used to create thumbnail and web-ready versions of images using the thumbnail maintenance tool, if used. | +| [**owner**](http://ns.adobe.com/xap/1.0/rights/Owner) | Text (250) | The legal owner of the media resource. | +| photographer | Text (100) | The creator of the media resource. | +| photographerUid | Integer (10) | The unique number assigned to the Symbiota portal user who created the media resource. Note that this can only be populated in cases when the photographer has a user account in the portal. | +| referenceUrl | Text (255) | A link to a URL or page that features the media resource in the original software. | +| [**rights**](http://dublincore.org/usage/terms/history/#rightsT-001) | Text (255) | The rights applied to the media resource dictating appropriate reuse of the item. For example, a [Creative Commons license](https://creativecommons.org/share-your-work/cclicenses/) may be applied here.| +| sortOccurrence | Integer (11) | The sort order of the media resource as it will appear on the page related to the occurrence record. Lower numbers will be displayed before higher numbers.| +| sourceIdentifier | Text (150) | A unique identifier belonging to the media resource provided by the source of the media item. | +| thumbnailUrl | Text (255) | A thumbnail-sized version (e.g., ~300 pixels in the widest dimension) of the media resource (if an image) to be shown quickly in search results.| +| url | Text (255) | A web-ready version of the media item (if an image), such as a JPG no larger than 2 MB. This is the version that is displayed as "medium resolution" in the occurrence editor.| diff --git a/content/coll_manager/restore/_index.en.md b/content/coll_manager/restore/_index.en.md index 7eef5d3b..73fed2a9 100644 --- a/content/coll_manager/restore/_index.en.md +++ b/content/coll_manager/restore/_index.en.md @@ -1,7 +1,7 @@ --- title: "Restoring your Database" date: 2021-12-15 -lastmod: 2024-05-10 +lastmod: 2025-01-31 draft: false weight: 168 authors: ["Katie Pearson"] @@ -11,9 +11,9 @@ keywords: ["restore","replace","upload"] In the case of catastrophic database error (e.g., erroneous batch edit that cannot be easily reversed), you can replace your entire database by uploading a Darwin Core Archive (DwC-A). Note that you need to have recently [downloaded a copy of your database](https://biokic.github.io/symbiota-docs/coll_manager/download/) with which you can replace your current database. To replace your database, navigate to the Administration Control Panel (My Profile > Occurrence Management > name of collection) and click “Restore Backup File” under the General Maintenance Tasks. You can then click Choose File and select a DwC-A with which to replace your dataset. - * If your DwC-A contains an “identifications” file, make sure that the "Restore Determination History" box is checked. - * If your DwC-A contains a “multimedia” file, make sure that the "Restore Images" box is checked. Click Analyze File. + * If your DwC-A contains an "identifications" file, make sure that the "Restore Determination History" box is checked. + * If your DwC-A contains a "multimedia" file, make sure that the "Restore Media Links" box is checked. Click Analyze File. -The file will take some time to load and process. Once this is done, a report called “Final transfer” will be displayed at the bottom of the screen. This report will show you how many records will be updated, how many records are new, how many identifications/determinations will be added, and how many records have images. **_Ensure that these numbers are as expected._** You can preview these records by clicking the table icon to the immediate right of the desired dataset (circled on next screenshot), or you can download these records as a CSV by clicking the two boxes icon to the far right of the desired dataset (in a square on next screenshot). Once you are satisfied that the records will be properly uploaded, click the "Transfer Records to Central Specimen Table" button. **Note that this change is _permanent_ and cannot be undone!** +The file will take some time to load and process. Once this is done, a report called “Final transfer” will be displayed at the bottom of the screen. This report will show you how many records will be updated, how many records are new, how many identifications/determinations will be added, and how many records have media links (e.g., images). **_Ensure that these numbers are as expected._** You can preview these records by clicking the table icon to the immediate right of the desired dataset (circled on next screenshot), or you can download these records as a CSV by clicking the two boxes icon to the far right of the desired dataset (in a square on next screenshot). Once you are satisfied that the records will be properly uploaded, click the "Transfer Records to Central Specimen Table" button. **Note that this change is _permanent_ and cannot be undone!** ![Final Transfer Screen](/symbiota-docs/images/restoredatafinaltransfer.jpg) diff --git a/content/coll_manager/stats/_index.en.md b/content/coll_manager/stats/_index.en.md index 2a986ff7..c52207e8 100644 --- a/content/coll_manager/stats/_index.en.md +++ b/content/coll_manager/stats/_index.en.md @@ -7,7 +7,7 @@ keywords: ["statistics","number of specimens","reports"] --- {{< notice info >}} - This page describes how you can find information about how many occurrences and images you have in your collection. + This page describes how you can find information about how many occurrences and media links (e.g., images) you have in your collection. {{}} ### Viewing Collection Statistics @@ -19,8 +19,8 @@ keywords: ["statistics","number of specimens","reports"] Statistics relating to the number of specimens, images, georeferences, and taxa within a collection can be found on that collection's Collection Profile page. An example collection profile is shown in the screenshot below and can be found [here](https://cch2.org/portal/collections/misc/collprofiles.php?collid=12). The collection statistics are found at the bottom of the page and include: * Number of total records * Number of records that are georeferenced -* Number of records that have associated images -* Total number of images in the collection +* Number of records that have associated media +* Total number of media resources in the collection * Number of specimens that are identified at least to the level of species * Number of families, genera, species, and total taxa that represented in the collection (NOTE: these numbers are calculated using only taxonomic names that have been indexed to the taxonomic thesaurus) @@ -38,6 +38,6 @@ Collection statistics are generated on command and are not created "on the fly". To view statistics regarding the processing statuses in your collection, navigate to your Administration Control Panel (My Profile > Occurrence Management > name of collection), then click Processing Toolbox. Click the Reports tab. A table will be displayed that shows you the number of specimens in each processing status. To view occurrences one by one, click the edit (pencil) icon in the **Count** column. To view occurrences as a list, click the table icon in the **Count** column. -This page will also show you how many of your occurrences do not have linked images and how many lack skeletal data (i.e., a value in the Scientific Name field). +This page will also show you how many of your occurrences do not have linked media resources and how many lack skeletal data (i.e., a value in the Scientific Name field). ![Reports Tab in Processing Toolbox](/symbiota-docs/images/reportstab.PNG) diff --git a/content/coll_manager/upload/_index.en.md b/content/coll_manager/upload/_index.en.md index 157addb9..a13c2ff3 100644 --- a/content/coll_manager/upload/_index.en.md +++ b/content/coll_manager/upload/_index.en.md @@ -17,7 +17,7 @@ keywords: ["data upload","data import","file upload","IPT"] There are several options for uploading data into a Symbiota portal: * **Full Text File Upload:** Use this upload type if you will provide a comma-separated value (CSV) or tab-separated value (TSV) file containing ALL fields of your occurrence data. You can convert an Excel document into a CSV file by clicking Save As, then selecting comma-delimited (CSV) from the file types. **Note that, if data exists in the portal for any of the occurrences you are uploading, those data will be overwritten by the incoming data.** To upload partial records, use a Skeletal File Upload. * **Skeletal File Upload:** Use this upload type if you will provide a CSV or TSV file containing data from only a few fields (e.g., georeferences or other ancillary data). **Note that this upload type can only fill in fields that are currently _empty_ in the portal.** The data provided in a skeletal file upload will NOT overwrite existing data in the database, so any pre-existing data in the desired fields must be deleted if you wish to replace it with the data from the skeletal file. -* **Darwin Core Archive Manual Upload:** Use this upload type if the data you wish to upload is in the format of a [Darwin Core Archive](http://en.wikipedia.org/wiki/Darwin_Core_Archive). A Darwin Core Archive (DwC-A) is a data standard that is commonly used to package species occurrence data into a single, self-contained dataset. A DwC-A includes metadata, a file of occurrence data, and, often, files for determinations (identifications) and images. +* **Darwin Core Archive Manual Upload:** Use this upload type if the data you wish to upload is in the format of a [Darwin Core Archive](http://en.wikipedia.org/wiki/Darwin_Core_Archive). A Darwin Core Archive (DwC-A) is a data standard that is commonly used to package species occurrence data into a single, self-contained dataset. A DwC-A includes metadata, a file of occurrence data, and, often, files for determinations (identifications) and media links (e.g., images). * **IPT Resource / Darwin Core Archive Provider:** Use this upload type if you will provide a URL to an existing Darwin Core Archive published on the web, such as one provided through an IPT. * **NfN File Upload:** Use this upload type if you will provide a CSV file produced from Notes from Nature. * **Direct Database Mapping:** @@ -75,7 +75,7 @@ If you have already created an import profile, or if you have been instructed to 4. Select the radio button for the name of the profile you would like to use for your import (if you just created an import profile, use that one). 5. Click the Initialize Upload button. 6. Click the Choose File button and select the Darwin Core Archive (packaged as a zip file) that you would like to upload. Then click the Analyze File button. -7. On the resulting page, you will have the option to view and/or verify the mappings of the incoming (1) occurrences file, (2) identification history file (if it exists), and (3) images file (if it exists). If one or more of these files does not exist in the incoming DwC-A, the checkbox to the left of it will be grayed out. To view or verify the mappings, click "view details" to the right of the file you wish to view. +7. On the resulting page, you will have the option to view and/or verify the mappings of the incoming (1) occurrences file, (2) identification history file (if it exists), and (3) multimedia file (if it exists). If one or more of these files does not exist in the incoming DwC-A, the checkbox to the left of it will be grayed out. To view or verify the mappings, click "view details" to the right of the file you wish to view. ![Darwin Core Import Profile Mapping Page](/symbiota-docs/images/dwc_import_profile.JPG) diff --git a/content/coll_manager/upload/fields/_index.en.md b/content/coll_manager/upload/fields/_index.en.md index add53be8..c09822c6 100644 --- a/content/coll_manager/upload/fields/_index.en.md +++ b/content/coll_manager/upload/fields/_index.en.md @@ -31,7 +31,7 @@ For more information about data fields, also see our [Symbiota Data Fields](http | Name | Type | Notes | |-|-|-| | associatedCollectors | Text (255) | All collectors except the primary collector, separated by commas or semicolons. | -| [_associatedMedia_](https://dwc.tdwg.org/terms/#dwc:associatedMedia) | Text (255) | URL to jpg images, delimited by commas or semicolons. More information about uploading images can be found on [this page](https://biokic.github.io/symbiota-docs/editor/images/upload/). | +| [_associatedMedia_](https://dwc.tdwg.org/terms/#dwc:associatedMedia) | Text (255) | URL to media resources, delimited by commas or semicolons. More information about uploading links to media resources (e.g., images) can be found on [this page](https://biokic.github.io/symbiota-docs/editor/images/upload/). | | [_associatedSequences_](https://dwc.tdwg.org/terms/#dwc:associatedSequences) | Text (65,535) | **Note:** This field is not yet accessible in the occurrence editor.| | [_associatedTaxa_](https://dwc.tdwg.org/terms/#dwc:associatedTaxa) | Text (65,535) | Associated taxa delimited by commas or semicolons | | authorInfraspecific | Text | The authorship of the infraspecific epithet, if different than the authorship of the specific epithet. If you do not provide authorships, authorships will be automatically assigned according to the taxonomic thesaurus (if the name is found in the thesaurus). See also specify:subspecies_author, specify:variety_author, and specify:forma_author. | diff --git a/content/editor/add/full/_index.en.md b/content/editor/add/full/_index.en.md index 2c408bc2..bc357bbb 100644 --- a/content/editor/add/full/_index.en.md +++ b/content/editor/add/full/_index.en.md @@ -16,6 +16,6 @@ Navigate to your Data Editor Control Panel (My Profile > Occurrence Management > To learn more about the data fields available in Symbiota, visit [this page](https://biokic.github.io/symbiota-docs/editor/edit/fields/). {{}} -Before you click Add record to create the new record, you can select one of three options for the next action you will perform, shown below. Go to New Record and Carryover Locality Information is useful for entering data from a single collection event that will share locality information. Remain on Editing Page should be used when the user wishes to double-check the record or add supplementary information such as images or annotations. +Before you click Add record to create the new record, you can select one of three options for the next action you will perform, shown below. Go to New Record and Carryover Locality Information is useful for entering data from a single collection event that will share locality information. Remain on Editing Page should be used when the user wishes to double-check the record or add supplementary information such as media resources (e.g., images) or annotations. ![Options for Adding Records](/symbiota-docs/images/newrecordoptions.png) diff --git a/content/editor/add/skeletal/_index.en.md b/content/editor/add/skeletal/_index.en.md index 07cf3d67..5ebef2e1 100644 --- a/content/editor/add/skeletal/_index.en.md +++ b/content/editor/add/skeletal/_index.en.md @@ -40,7 +40,7 @@ This tool can be used to collect basic collection information, for example, duri ![Skeletal Records Added](/symbiota-docs/images/skeletaladded.png) {{< notice note >}} - In the event that a user needs to edit a previously entered skeletal record, you can click the catalog number of the record as it is listed in the Records box below the Skeletal Data box. Note that this list will disappear if the page is refreshed. You can also add an image to the record from this page by clicking the icon to the right of the listed catalog number. + In the event that a user needs to edit a previously entered skeletal record, you can click the catalog number of the record as it is listed in the Records box below the Skeletal Data box. Note that this list will disappear if the page is refreshed. You can also add an image or other media resource to the record from this page by clicking the icon to the right of the listed catalog number. {{}} Further clarification about the Skeletal Data Entry tool can be found here: [SERNEC Skeletal Data Entry Guide](https://herbarium.appstate.edu/sites/herbarium.appstate.edu/files/sernec-tcn.skeletaldataentryv3.pdf) diff --git a/content/editor/edit/duplicates/_index.en.md b/content/editor/edit/duplicates/_index.en.md index 481dabf6..85bc7bf6 100644 --- a/content/editor/edit/duplicates/_index.en.md +++ b/content/editor/edit/duplicates/_index.en.md @@ -57,6 +57,6 @@ Checking this box and then clicking one of the additional options will create a This option is only available if the identified duplicate belongs to the same collection that you are currently editing. Clicking this option will take you to the occurrence editor page for the duplicate record so you can view it (e.g., if you want to verify the data or view the image). Once you have looked at the image, if you want to transfer any of the data into the record you are working on, you will need to click the "Duplicates" button on the record that you were editing again. #### Merge Records -This option is only available if the identified duplicate belongs to the same collection that you are currently editing. If you click this option, the two records will be merged together. **The record in the pop-up window will be prioritized over data in your occurrence editor.** For example, if the record listed in the pop-up window has "USA" in the country field, and the record in the occurrence editor has "United States" in the country field, the merged record will have "USA" in the country field. Fields that are empty in one of the two records will be filled in with the data from the record that has data in that field. All images and linked resources will be included in the merged record. All unique determinations will be included in the merged record with the exception of any "current determination" belonging to the record in the occurrence editor, which will be discarded. As a result, you will have one current determination (belonging to the record in the pop-up window) and all other previous determinations associated with the record. For this reason, it is a good idea to check the Determinations tab of the merged record before moving on. +This option is only available if the identified duplicate belongs to the same collection that you are currently editing. If you click this option, the two records will be merged together. **The record in the pop-up window will be prioritized over data in your occurrence editor.** For example, if the record listed in the pop-up window has "USA" in the country field, and the record in the occurrence editor has "United States" in the country field, the merged record will have "USA" in the country field. Fields that are empty in one of the two records will be filled in with the data from the record that has data in that field. All media resources (e.g., images) and linked resources will be included in the merged record. All unique determinations will be included in the merged record with the exception of any "current determination" belonging to the record in the occurrence editor, which will be discarded. As a result, you will have one current determination (belonging to the record in the pop-up window) and all other previous determinations associated with the record. For this reason, it is a good idea to check the Determinations tab of the merged record before moving on. ![Possible EXACT Duplicate results within collection](/symbiota-docs/images/exactdupeincolfull.PNG) diff --git a/content/editor/edit/tabs/_index.en.md b/content/editor/edit/tabs/_index.en.md index a9db2c58..68d5c9a4 100644 --- a/content/editor/edit/tabs/_index.en.md +++ b/content/editor/edit/tabs/_index.en.md @@ -20,7 +20,7 @@ Upon opening the Record Editor page, you will see 4-5 tabs, depending on your le **Determination History** – where annotations are shown and can be entered. Annotations can also be batch uploaded from separate files. See [Annotations](https://biokic.github.io/symbiota-docs/editor/edit/annotations/) -**Images** – provides information on image(s) associated with the record. See [Images](https://biokic.github.io/symbiota-docs/editor/images/) +**Media** – provides information on media resources associated with the record. See [Images](https://biokic.github.io/symbiota-docs/editor/images/) **Material Sample** - allows for association of multiple material sample records per specimen occurrence. For this tab to be visible, it must be configured per portal and activated per collection. Contact your Collection Administrator for more information. See [Material Sample](https://biokic.github.io/symbiota-docs/editor/materialsample/) diff --git a/content/editor/images/_index.en.md b/content/editor/images/_index.en.md index 8fb2be33..e5ce1cbf 100644 --- a/content/editor/images/_index.en.md +++ b/content/editor/images/_index.en.md @@ -1,7 +1,7 @@ --- -title: "Images" +title: "Images & Other Media" date: 2021-10-06 -lastmod: 2024-02-13 +lastmod: 2025-01-31 draft: false authors: ["Ed Gilbert","Katie Pearson"] weight: 90 @@ -9,29 +9,36 @@ keywords: ["images"] --- {{< notice info >}} - This page describes the types of images that are available through Symbiota portals. + This page describes the types of media that are supported by Symbiota portals. {{}} -There are three catefories of images that can be linked to a Symbiota portal: +{{< notice tip >}} + As of Symbiota version 3.2, Symbiota portals support audio files! For this reason, most tools are now labeled **media** or **multimedia** tools, rather than "image tools," as in previous versions of Symbiota. **Media** refers to any audiovisual media such as images or audio files; however, video files are not currently supported. +{{}} + +There are three categories of media that can be linked to a Symbiota portal: {{< tabs >}} - {{< tab "Field Images without Location" >}} - Images without specific locality information (e.g. lat/long coordinates) are linked only to the scientific name of the organism. These images can be viewed through Taxon Profile Pages, which have general information such as descriptions, distribution maps, synonyms, and common names. Field images are uploaded and managed through the Taxon Profile pages by users with Taxon Profile editing permissions. Field images with specific locality details (e.g. coordinates) can be loaded as Image Vouchers (see "Field Images with Location" tab). See Uploading Images for more details. - {{}} + {{< tab "Specimen Images/Media" >}} + Media (e.g., images) relating to physical specimens should be linked to their respective specimen records. Specimen-linked media are available both from the Occurrence Details page and the Taxon Profile page for the taxon associated with the most recent determination. If the specimen identification is annotated, the taxonomic identification of the media resource will be automatically re-mapped to that taxon. Specimen-linked media can be added through the Occurrence Editor or in batch via multiple processes. - {{< tab "Field Images with Location" >}} - Field images with specific locality information can adequately serve as vouchers for field observations of many birds, mammals, and easy-to-identify plants. In some instances, they may actually be preferable, for instance if the organism is rare or the observer does not have the appropriate collecting permit. These images are similar to georeferenced specimen records in that they are searchable occurrence records that place a dot on the species distribution maps. There are, however, some taxonomic groups that typically require microscopic or chemical analysis for accurate identification (e.g. lichens, bryophytes, fungi). For such organisms, field images will have limited value. For this reason, some data portals might not allow the submission of observations without a physical specimen.

- Image Vouchers are displayed on both the Occurrence Details and the Taxon Profile pages. Image-supported observations can be uploaded using the Observation Submission page. Up to three images can be submitted for a single observation. Data fields required for an image to qualify as a voucher include: observer name, observation date, country, state, locality description, latitude, longitude, and at least one image. Contact your data portal administrator for information on whether observations are allowed and the necessary protocols for submitting an observation. Some portals require the review of a tutorial before one is authorized to submit an observation. - See Uploading Images for more details. + See Uploading Images/Media for more details. {{}} - {{< tab "Specimen Images" >}} - Images of physical specimens should be linked to their respective specimen records. Specimen images are available both from the Occurrence Details page and the Taxon Profile page for the taxon associated with the most recent determination. If the specimen identification is annotated, the identification of the image will be automatically re-mapped to that taxon. Specimen images can be added through the Occurrence Editor or in batch via multiple processes. + {{< tab "Field Media without Location" >}} + Media without specific locality information (e.g. lat/long coordinates) are linked only to the scientific name of the organism. These media resources can be viewed through Taxon Profile Pages, which have general information such as descriptions, distribution maps, synonyms, and common names. Field media are uploaded and managed through the Taxon Profile pages by users with Taxon Profile editing permissions. Field media with specific locality details (e.g. coordinates) can be loaded as Media Vouchers (see "Field Media with Location" tab). See Uploading Images/Media for more details. + {{}} + {{< tab "Field Media with Location" >}} + Field media with specific locality information can adequately serve as vouchers for field observations of many birds, mammals, and easy-to-identify plants. In some instances, they may actually be preferable, for instance if the organism is rare or the observer does not have the appropriate collecting permit. These media resources are similar to georeferenced specimen records in that they are searchable occurrence records that place a dot on the species distribution maps. There are, however, some taxonomic groups that typically require microscopic or chemical analysis for accurate identification (e.g. lichens, bryophytes, fungi). For such organisms, field images will have limited value. For this reason, some data portals might not allow the submission of observations without a physical specimen.

- See Uploading Images for more details. + Image Vouchers are displayed on both the Occurrence Details and the Taxon Profile pages. Image-supported observations can be uploaded using the Observation Submission page. Up to three images can be submitted for a single observation. Data fields required for an image to qualify as a voucher include: observer name, observation date, country, state, locality description, latitude, longitude, and at least one image. Contact your data portal administrator for information on whether observations are allowed and the necessary protocols for submitting an observation. Some portals require the review of a tutorial before one is authorized to submit an observation. + See Uploading Images/Media for more details. {{}} + + + {{}} {{< youtube m1HHN4g4NGg >}} diff --git a/content/editor/images/batch/_index.en.md b/content/editor/images/batch/_index.en.md index a797a06a..8d48489b 100644 --- a/content/editor/images/batch/_index.en.md +++ b/content/editor/images/batch/_index.en.md @@ -1,7 +1,7 @@ --- -title: "Batch Uploading Images" +title: "Batch Uploading Images/Media" date: 2021-12-14 -modified: 2024-10-18 +modified: 2025-01-31 weight: 2 draft: false authors: ["Ed Gilbert","Ben Brandt","Katie Pearson"] @@ -10,15 +10,15 @@ keywords: ["images"] --- {{< notice info >}} - This page describes some workflows for batch uploading images into a Symbiota portal. + This page describes some workflows for batch uploading images or other media resources into a Symbiota portal. {{}} -Symbiota portals do not necessarily store images, rather, they store links to where images can be accessed via the web. For this reason, there are many ways that images can be linked to occurrence records in the portal. Any storage solution that can provide a web-accessible URL to an image can be used to link images to occurrences in a Symbiota portal. +Symbiota databases do not physically store media resources such as images, rather, they store links to where media resources can be accessed via the web. For this reason, there are many ways that media resources can be linked to occurrence records in the portal. Any storage solution that can provide a web-accessible URL to an media resource can be used to link images to occurrences in a Symbiota portal. -#### Image Storage through the Symbiota Support Hub +#### Media Storage through the Symbiota Support Hub -For relatively small collections with little to no IT support, the Symbiota Support Hub (SSH) may be able to web-host the jpeg versions (<10 MB) of images for display in a Symbiota portal. In this case, images are uploaded to Globus and transferred to SSH-managed servers. The URLs generated by these servers are then linked to your records in a Sybmiota portal. To determine whether this is possible for your collection, contact the [Symbiota Support Hub](mailto:help@symbiota.org). +For collections with little capacity to host their own media resources, the Symbiota Support Hub (SSH) may be able to host web-ready versions (e.g., jpegs, for image files) of media resources for access via a Symbiota portal. In this case, media resources (largely images) are uploaded to Globus and transferred to SSH-managed servers. The URLs generated by these servers are then linked to your records in a Sybmiota portal. To determine whether this is possible for your collection, contact the [Symbiota Support Hub](mailto:help@symbiota.org). -#### Image Storage through an Institutional Server +#### Media Storage through an Institutional Server -If your institution has the ability to serve images in a web-accessible format, these URLs can be easily linked to their occurrences in your portal through a batch processing script. Contact your portal administrator or the Symbiota Support Hub for more information or to set up this workflow. +If your institution has the ability to serve media resources in a web-accessible format, these URLs can be easily linked to their occurrences in your portal through a batch processing script. Contact your portal administrator or the Symbiota Support Hub for more information or to set up this workflow. diff --git a/content/editor/images/delete/_index.en.md b/content/editor/images/delete/_index.en.md index 09bb4854..7aec1529 100644 --- a/content/editor/images/delete/_index.en.md +++ b/content/editor/images/delete/_index.en.md @@ -1,42 +1,43 @@ --- -title: "Deleting Images or Transferring Between Records" +title: "Deleting or Transferring Images/Media" date: 2021-11-28 +latmod: 2025-01-31 weight: 2 authors: ["Katie Pearson"] keywords: ["images"] --- {{< notice info >}} - This page describes how to transfer images to other records in your collection or how to delete images associated with a record. + This page describes how to transfer media resources to other records in your collection or how to delete media resources associated with a record. {{}} -#### Transferring an Image to Another Record -1. Navigate to the occurrence record that has the image you would like to transfer. (e.g., My Profile > Occurrence Management > name of collection > Edit Existing Occurrence Records > use record search form to find specific occurrence). +#### Transferring a Media Resource to Another Record +1. Navigate to the occurrence record that has the media resource you would like to transfer. (e.g., My Profile > Occurrence Management > name of collection > Edit Existing Occurrence Records > use record search form to find specific occurrence). 2. Open the occurrence record in the Occurrence Editor (see screenshot below). -3. Click the Images tab. +3. Click the Media tab. -![Images Tab](/symbiota-docs/images/imagestab.PNG) +![Media Tab](/symbiota-docs/images/mediatab.jpg) -4. Click the pencil icon to the right of the image you would like to transfer. -5. If you would like to transfer the image to a brand new record, rather than a record that already exists, scroll down to the box labeled **Link to a New Blank Occurrence Record within Collection** and click the "Link to New Occurrence" button. - * The SymbiotaID number associated with the new record you have created with the image will be displayed at the top of the page after you click this button. To navigate to that record, click the blue SymbiotaID number. -6. If you would like to transfer the image to a record that already exists, scroll down to the box labeled **Remap to Another Specimen**. +4. Click the pencil icon to the right of the media resource you would like to transfer. +5. If you would like to transfer the media resource to a brand new record, rather than a record that already exists, scroll down to the box labeled **Link to a New Blank Occurrence Record within Collection** and click the "Link to New Occurrence" button. + * The SymbiotaID number associated with the new record you have created with the media resource will be displayed at the top of the page after you click this button. To navigate to that record, click the blue SymbiotaID number. +6. If you would like to transfer the media resource to a record that already exists, scroll down to the box labeled **Remap to Another Specimen**. 7. You can either enter the SymbiotaID number for the record (if you have it on hand) or use the Occurrence Linking Aid (where you can search by catalog number, collector, and/or collector number). To do the latter, click "Open Occurrence Linking Aid" to the right of the field. -8. In the pop-up window, enter the search terms you would like to use to find the occurrence to which you would like to link the image. You can include several terms in this search concurrently. Then click the Search Occurrences button to see the search results. +8. In the pop-up window, enter the search terms you would like to use to find the occurrence to which you would like to link the media resource. You can include several terms in this search concurrently. Then click the Search Occurrences button to see the search results. 9. If there are results of your search, they will be listed below the **Voucher Search Pane** as shown below. To select one of the listed occurrences for linking, click Select Occurrence Record. This will close the window and import that record's SymbiotaID number into the **Remap to Another Specimen** panel. - * If you don't find the record you are looking for, try using different search terms. If the record does not exist, you can click the Create New Occurrence button to create a brand new occurrence for the image. + * If you don't find the record you are looking for, try using different search terms. If the record does not exist, you can click the Create New Occurrence button to create a brand new occurrence for the media resource. ![Occurrence Linking Aid](/symbiota-docs/images/occlinkingaid.PNG) -10. Back on the images tab of the Occurrence Editor page, click the Remap Image button. +10. Back on the Media tab of the Occurrence Editor page, click the Remap Resource button. {{< notice note >}} - Any data associated with that image (e.g., its catalog number) will NOT be transferred along with the image. You will need to copy over this information in another way, if applicable. + Any data associated with that media resource (e.g., its catalog number) will NOT be transferred along with the media resource. You will need to copy over this information in another way, if applicable. {{}} -#### Deleting an Image +#### Deleting a Media Resource 1. Complete steps 1-4 in the instructions above. -2. Scroll down to the box labeled **Delete Image**. - * If your images are stored on ASU servers (i.e., you upload them to Dropbox or otherwise transfer them to ASU), check the "Remove image from server" box. Otherwise, leave this box unchecked - * If your images are stored on another server, such as CyVerse, leave the "Remove image from server" box unchecked. +2. Scroll down to the box labeled **Delete Resource**. + * If your media resources are stored on Symbiota Support Hub servers (i.e., you upload them via Globus or directly through the Media tab), check the "Remove resource from server" box. Otherwise, leave this box unchecked. + * If your media resources are stored on another server, such as an institutional server, leave the "Remove resource from server" box unchecked. diff --git a/content/editor/images/tag/_index.en.md b/content/editor/images/tag/_index.en.md index 1df2b996..a2d5a82b 100644 --- a/content/editor/images/tag/_index.en.md +++ b/content/editor/images/tag/_index.en.md @@ -1,38 +1,38 @@ --- -title: "Tagging Images" +title: "Tagging Images/Media" date: 2021-12-13 -lastmod: 2024-03-04 +lastmod: 2025-01-31 draft: false weight: 6 authors: ["Katie Pearson"] -keywords: ["image tags","image annotation"] +keywords: ["image tags","image annotation","media"] --- {{< notice info >}} - This page describes how to tag images of occurrences. + This page describes how to tag media resources (e.g., images) linked to occurrences. {{}} -### Tagging individual images +### Tagging individual media resources -Occurrence images can be tagged with important metadata about what is contained within that image. For example, a specimen can be marked as representing an adult organism or an immature organism. Some possible tags are shown in the image below: +Occurrence media resources can be tagged with important metadata about what is contained within that media resource. For example, a specimen image an be marked as representing an adult organism or an immature organism. Some possible tags are shown below: -![Image Tags](/symbiota-docs/images/imagetags.PNG) +![Media Resource Tags](/symbiota-docs/images/imagetags.PNG) -To tag an image, navigate to the occurrence to which that image belongs (see [this page](https://biokic.github.io/symbiota-docs/editor/edit/)). Then click the Images tab. Click the edit button ![Edit Button](/symbiota-docs/images/edit.png) and scroll down to the checklist of tags that you can add to the image. Click the Submit Image Edits button when complete. +To tag an media resource, navigate to the occurrence to which that media resource belongs (see [this page](https://biokic.github.io/symbiota-docs/editor/edit/)). Then click the Media tab. Click the pencil icon next to the Taxonomic Name field and scroll down to the checklist of tags that you can add to the media resource. Click the Submit Resource Edits button when complete. -### Batch tagging images +### Batch tagging media resources -1. Navigate to the Image Search interface in your portal. This is usually listed on main menu of your portal, potentially nested in an "Images" dropdown section. If you can't find it here, navigate to your Sitemap and click "Interactive Search Tool" under the Image Library header. +1. Navigate to the Media Search interface in your portal. This is usually listed on main menu of your portal, potentially nested in an "Images" dropdown section. If you can't find it here, navigate to your Sitemap and click "Interactive Search Tool" under the Media Library header. {{< notice note >}} - Even though you access this tool through the Image Search interface, you will need editor permissions to tag images in the search results. + Even though you access this tool through the Media Search interface, you will need editor permissions to tag images in the search results. {{}} -2. Enter the search criteria for the images you would like to tag in the Search Criteria box. - * To select images from a specific collection, select the "Specimen/Vouchered Images" from the **Image Type** dropdown box and then use the checkboxes to select the collection(s) from which you would like to see images. Click the plus icon to expand the lists of collections, if applicable. -3. Click the Load Images button. +2. Enter the search criteria for the media resources you would like to tag in the Search Criteria box. + * To select media resources from a specific collection, select the "Specimen/Vouchered Media" from the **Media Type** dropdown box and then use the checkboxes to select the collection(s) from which you would like to see media resources. Click the plus icon to expand the lists of collections, if applicable. +3. Click the Load Media button. 4. Click the pencil icon in the top right corner of the Search Criteria box to toggle the batch tagging interface ON. A new box labeled Action Panel will show up below the Search Criteria box. -5. Select the Image Tag from the dropdown list that you would like to apply, then check the boxes next to the images to which you would like to apply that tag. -6. Click the Batch Assign Tag button to apply that tag to the selected images. +5. Select the Media Tag from the dropdown list that you would like to apply, then check the boxes next to the media resources to which you would like to apply that tag. +6. Click the Batch Assign Tag button to apply that tag to the selected media resources. -![Batch Image Tagging Interface](/symbiota-docs/images/batchtag.PNG) \ No newline at end of file +![Batch Media Tagging Interface](/symbiota-docs/images/batchtag.PNG) \ No newline at end of file diff --git a/content/editor/images/upload/_index.en.md b/content/editor/images/upload/_index.en.md index ff032241..2c30b323 100644 --- a/content/editor/images/upload/_index.en.md +++ b/content/editor/images/upload/_index.en.md @@ -1,7 +1,7 @@ --- -title: "Uploading Images" +title: "Uploading Images/Media" date: 2021-10-06 -lastmod: 2024-10-04 +lastmod: 2025-01-31 weight: 10 draft: false authors: ["Ed Gilbert","Ben Brandt","Katie Pearson"] @@ -9,36 +9,36 @@ keywords: ["images"] --- {{< notice info >}} - This page describes how to upload individual *field* and *specimen* images using the Symbiota portal interface. Technically, images are **not** stored _within_ a Symbiota database. Instead, the URLs of the images are stored. Thus, it is also possible to link images that are stored in external servers. For information about the latter option, visit the [Batch Adding/Linking Images](https://biokic.github.io/symbiota-docs/coll_manager/images/batch/) page. + This page describes how to upload individual *field* and *specimen*-related media resources (e.g., images) using the Symbiota portal interface. Technically, media resources are **not** stored _within_ a Symbiota database. Instead, the URLs of the media resources are stored. Thus, it is also possible to link media resources that are stored in external servers. For information about the latter option, visit the [Batch Adding/Linking Images](/symbiota-docs/coll_manager/images/batch/) page. {{}} -Images associated with records in a Symbiota portal may be **Externally Hosted** or **Internally Hosted**. +Media resources associated with records in a Symbiota portal may be **Externally Hosted** or **Internally Hosted**. -* **Externally Hosted** images are those stored on servers that are unrelated to the Symbiota portal (e.g., are housed at another institution). These external servers provide image links, which can then be loaded into the Symbiota database. +* **Externally Hosted** media resources are those stored on servers that are unrelated to the Symbiota portal (e.g., are housed at another institution). These external servers provide media links, which can then be loaded into the Symbiota database. -* **Internally Hosted** images are those stored on servers that are write-accessible to the Symbiota portal server. For example, if you coordinate with Arizona State University to batch upload images to one of their hosted portals (e.g., SEINet, Bryophyte Portal), your images are Internally Hosted. +* **Internally Hosted** media resources are those stored on servers that are write-accessible to the Symbiota portal server. For example, if you coordinate with the Symbiota Support Hub to batch upload images to one of their hosted portals (e.g., SEINet, Bryophyte Portal), your images are Internally Hosted. -There are three catefories of images that can be linked to a Symbiota portal. Instructions for uploading individual images of each of these types are provided below. **The below instructions assume that your portal is configured with an image directory that allows upload of images directly through the interface.** This is the case with most portals, but if you run into issues, you may need to contact a portal administrator. +There are three catefories of media resources that can be linked to a Symbiota portal. Instructions for uploading individual media resources of each of these types are provided below. **The below instructions assume that your portal is configured with an media directory that allows upload of media resources directly through the interface.** This is the case with most portals, but if you run into issues, you may need to contact a portal administrator. -### Individual specimen images +### Individual specimen media resources 1. Log in to your account in the portal. 2. Navigate to the Occurrence Editor page of the specimen to which you would like to add an image (My Profile > Occurrence Management > name of collection > Edit Existing Occurrence Records > conduct search for specimen) -3. Click the Images tab. +3. Click the Media tab. -![Images Tab](/symbiota-docs/images/imagestab.png) +![Media Tab](/symbiota-docs/images/mediatab.jpg) -4. If an image has already been added to the specimen, and you wish to add another click the green plus sign at the top right of the window. Otherwise, the image uploading interface will be highlighted in yellow on this page. -5. Click the Choose File button and navigate to the image file you wish to upload. If you instead have a URL to the image, you can click Enter URL and paste the URL into the resulting field instead. -6. Enter any additional information, if desired, in the other image uploading fields. +4. If an media resource has already been added to the specimen, and you wish to add another click the add (plus sign) icon at the top right of the window. Otherwise, the media resource uploading interface will be highlighted in yellow on this tab. +5. Click the Choose File button and navigate to the file you wish to upload. If you instead have a URL to the media resource, you can click the Enter URL link and paste the URL into the resulting field instead. +6. Enter any additional information, if desired, in the other fields. {{< notice tip >}} - You can enter a number into the Sort field if you wish to define the order in which mutliple images will appear on the occurrence page. If you enter a number greater than 500 in the Sort field, that image will be displayed on the Occurrence Details page but on the Taxon Profile page for that taxon. This is ideal for poor-quality or sensitive images (e.g. road kills). + You can enter a number into the Sort field if you wish to define the order in which mutliple media resources will appear on the occurrence page. If you enter a number greater than 500 in the Sort field, that media resource will be displayed on the Occurrence Details page but not on the Taxon Profile page for that taxon. This is ideal for poor-quality or sensitive images (e.g. road kills). {{}} -7. Click the Submit New Image button. +7. Click the Submit New Resource button. -### Field image without location information +### Field media resource without location information Images without specific locality information (e.g. lat/long coordinates) are linked only to the scientific name of the organism. These images can be viewed on the Taxon Profile Page, which has general information such as descriptions, distribution maps, synonyms, and common names. To upload an image: @@ -50,18 +50,18 @@ Images without specific locality information (e.g. lat/long coordinates) are lin * Click Sitemap, then Taxonomic Tree Viewer or Taxonomy Explorer. Search for the taxon of interest and click its name. * Perform a quick search on the home page for the taxon of interest. 3. Click the pencil icon at the top right corner of the taxon page. -4. Click the Add Image tab. -5. Select the image file you would like to upload from Choose File, then enter any additional information in the provided fields. - * The **Sort Sequence** field allows you to determine the order of the images that will show up on the taxon profile. The higher the number, the further down the priority list the image will be. -7. Click the Upload Image button. -8. Field images are uploaded and managed through the Taxon Profile Editing interface. Users with Taxon Profile editing permissions can submit an image by clicking on the editing symbol located in the upper right of any Taxon Profile page, or through the image submission links available on the sitemap page. Field images with specific locality details (e.g. coordinates) can be loaded as Image Vouchers (see below). +4. Click the Add Media tab. +5. Select the media file you would like to upload from Choose File, then enter any additional information in the provided fields. + * The **Sort Sequence** field allows you to determine the order of the media resources that will show up on the taxon profile. The higher the number, the further down the priority list the media resource will be. +7. Click the Upload Media Resource button. +8. Field media resources (e.g., field images) are uploaded and managed through the Taxon Profile Editing interface. Users with Taxon Profile editing permissions can submit a media resource by clicking on the editing symbol located in the upper right of any Taxon Profile page, or through the image submission links available on the sitemap page. Field media with specific locality details (e.g. coordinates) can be loaded as Image Vouchers (see below). -### Image Vouchers (field images with location information) +### Media vouchers (field images with location information) -Field images with specific locality information can serve as vouchers for field observations of many birds, mammals, and easy-to-identify plants. There are, however, some taxonomic groups that typically require microscopic or chemical analysis for accurate identification (e.g. lichens, bryophytes, fungi). For such organisms, field images will have limited value. For this reason, some data portals might not allow the submission of observations without a physical specimen. +Field-based media with specific locality information can serve as vouchers for field observations of many birds, mammals, and easy-to-identify plants. There are, however, some taxonomic groups that typically require microscopic or chemical analysis for accurate identification (e.g. lichens, bryophytes, fungi). For such organisms, field-based media such as images will have limited value. For this reason, some data portals might not allow the submission of observations without a physical specimen. -It is particularly important that images intended as vouchers for an observation be of high quality and clearly display diagnostic morphology of the organism. Data fields required for an image to qualify as a voucher include: observer name, observation date, country, state, locality description, latitude, longitude, and at least one image. +It is particularly important that media resources intended as vouchers for an observation be of high quality and clearly demonstrate diagnostic morphology of the organism. Data fields required for an image to qualify as a voucher include: observer name, observation date, country, state, locality description, latitude, longitude, and at least one image. -As is the case with images of physical specimen, Image Vouchers are displayed on both the Occurrence Details and the Taxon Profile pages. Image-supported observations can be uploaded in a General Research Observation profile. The following video describes how to gain access to and submit observations to such a collection: +As is the case with images of physical specimen, Media Vouchers are displayed on both the Occurrence Details and the Taxon Profile pages. Media-supported observations can be uploaded in a General Research Observation profile. The following video describes how to gain access to and submit observations to such a collection: {{< youtube 4uj15JCzHg4 >}} diff --git a/static/images/batchtag.PNG b/static/images/batchtag.PNG index aed1ad0a..fa92d176 100644 Binary files a/static/images/batchtag.PNG and b/static/images/batchtag.PNG differ diff --git a/static/images/mediatab.jpg b/static/images/mediatab.jpg new file mode 100644 index 00000000..179434b7 Binary files /dev/null and b/static/images/mediatab.jpg differ