TITLE: Annotating PDF documents for the GeoArchive
AUTHORS: Sky Bristol

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides steps to catalog NI 43-101 Technical Reports within the Zotero reference management system and use PDF highlighting and annotation to identify specific citation metadata and other descriptive information from the texts. It is part of a body of work being developed to manage a GeoArchive digital library of important reference materials in minerals assessments, energy assessments, and other work of the US Geological Survey.</div></div>

[STEPS]
?. [Setup Collection in Zotero]
Setup a local collection for the reports/documents you want to start annotating in Zotero.
We have created a group library in Zotero that can be used for this work, or you may elect to work in a separate collection in your own library ("My Library" in the Zotero client). If you would like to use the GeoArchive Group Library, you must create a Zotero account and be granted access to the group. This will let you accomplish the rest of the steps from the group space, making your report items, files, and annotations immediately available to other members of the group.
?. [Setup Collection in Zotero]
Create collection
?. [Setup Collection in Zotero]
?. [Import Files to Zotero]
Copying the files into Zotero means that Zotero will place them into its own directory structure. This facilitates Zotero working with the files, linking to them with internal references, and other actions. For our purposes, this simply makes sure that we have all of the files in one place along with any metadata we can start developing for them so that we can move it all to a shared, group library.
?. [Import Files to Zotero]
Drag and drop files
?. [Establish Proper Item Types]
After dragging and dropping a batch of files into Zotero, you may see that some have been brought in as journal article type items while others are simply files that do not yet have a Zotero item created for them. Zotero defaults to "thinking" that everything is a journal article as this is the most common use case. We need to establish items for everything and set everything to the appropriate type. This section covers that work.
?. [Establish Proper Item Types]
Select files that were not processed to create items, right click, and select Create Parent Items from the list of options.
?. [Establish Proper Item Types]
Change all item types to "Report"
?. [Annotate PDF Documents]
We can now start annotating the PDFs documents stored with Zotero. Part of this will be developing a few fields of basic citation metadata. If the import process was able to successfully find things like title and authors, it is not necessary to annotate these elements separately. We already have them and can move that information into a shared library if we continue using Zotero in that capacity or export the information to include in another system. The following steps outline the approach to annotation that we can refine over time.
We will be evolving the annotation protocol over time to include more types of information content. If you have thoughts about the types of annotation that should be included as you go through this part of the protocol, please login with a protocols.io account and post your comments directly to the protocol.
?. [Annotate PDF Documents]
Open a PDF for annotation. Zotero should be set up to use your system default PDF reader. This will vary between operating systems and circumstances. You can change this setting in Zotero preferences if desired.You can usually either double-click on the item in the Library or open the "twisty" next to the item to view its file and double click that to open.
?. [Annotate PDF Documents]
Highlight and annotate title (if necessary)
Use title as the simple annotation for this element.
?. [Annotate PDF Documents]
Highlight and annotate dates for the publicationHighlight and annotate one or more of the following dates using these terms:- effective date- report date- publication date
?. [Annotate PDF Documents]
Highlight and annotate the project name
Use project as the simple annotation for this element
?. [Annotate PDF Documents]
Highlight and annotate companies (or institutions) operating the mineral development project and/or producing the reportHighlight and annotate one or more of the following company names/institutions using these terms:- report producer- project operator
The name of the company that produced the report is required in order to build a proper citation string for the report. The company operating the mine or development project should also be listed and will further aid in future work with the information.
?. [Annotate PDF Documents]
Highlight and annotate significant place names
Use place as the simple annotation for this element, highlighting and annotating as many places as are significant and useful in roughly geolocating the development project and associated geoscientific information.
?. [Annotate PDF Documents]
Highlight and annotate report authors
Use author as the simple annotation for this element
?. [Annotate PDF Documents]
Highlight and annotate latitude and longitude coordinates if provided
Use latitude and longitude as the annotations for these elements
?. [Annotate PDF Documents]
Highlight and annotate commodity names
Use commodity as the simple annotation for this element
?. [Saving and Processing]
Save the PDF file at the end of or during annotation. Depending on the platform and software used, this may be done automatically. The highlights and annotations will be saved with the Zotero copy of the file.
At this stage, the most important thing is simply to get the annotations started within the files. Don't worry that the metadata you've highlighted is not a part of the citation information in Zotero yet. We'll get to that point shortly through a software process that will need to extract the annotations from the texts and place it back into Zotero.If we do continue using the Zotero group library for a time, at least up to the limitation of 300MB of files per user, we can set up an automated process to extract the annotations and populate Report metadata content. This will follow the example outlined here but can be set up to run in the background.
?. [Annotate PDF Documents]
Highlight and annotate tables of data and other important details for further use of the reports in assessments and other practices. We will monitor and discuss development of annotation conventions over time to develop a reasonable vocabulary for identifying additional important elements in these and other documents.We will be employing a toolset for extracting tabular data and figures from these texts that we can improve on over time. It is not necessary to highlight an entire table or figure, but it will be helpful to highlight a title or caption for tables and figures of interest as well as providing a meaningful annotation.Annotations can also include further meaningful text to aid in the use of the material. Simple keyword types of indicators like we are using for identifying citation elements are useful for running extraction processes to classify particular information for use, but we can experiment with a convention for delimiters to incorporate a classifier for software to use along with a longer annotation for human consumption. For instance, something like the following might be a reasonable annotation on a particular table in a report. It tells a computer program that the table is of a particular type and then provides an opinion by the annotator for further investigation.
summary of mineral resources: This table shows a higher than expected concentration of potash than expected for this formation.